Clean up extra files from Mendeley imports

Follow-up to cdee741a6

.babelrc

@@ -5,7 +5,6 @@
   "ignore": [
     "resource/require.js",
     "chrome/content/zotero/include.js",
-    "resource/tinymce/tinymce.js",
     "chrome/content/zotero/xpcom/citeproc.js",
     "resource/csl-validator.js",
     "resource/react.js",
@@ -15,16 +14,7 @@
     "test/resource/*.js"
   ],
   "plugins": [
-    "syntax-flow",
     "syntax-jsx",
-    "syntax-async-generators",
-    "syntax-class-properties",
-    "syntax-decorators",
-    "syntax-do-expressions",
-    "syntax-export-extensions",
-    "syntax-flow",
-    "syntax-jsx",
-    "syntax-object-rest-spread",
     "transform-react-jsx",
     "transform-react-display-name",
     [
@@ -34,4 +24,4 @@
       }
     ]
   ]
-}
+}

.gitignore

@@ -1,4 +1,5 @@
 .DS_Store
 node_modules
 build
-.signatures.json
+.signatures.json
+tmp

.gitmodules

@@ -1,18 +1,24 @@
 [submodule "translators"]
 	path = translators
 	url = git://github.com/zotero/translators.git
+	branch = master
 [submodule "chrome/content/zotero/locale/csl"]
 	path = chrome/content/zotero/locale/csl
 	url = git://github.com/citation-style-language/locales.git
+	branch = master
 [submodule "styles"]
 	path = styles
 	url = git://github.com/zotero/bundled-styles.git
+	branch = master
 [submodule "test/resource/chai"]
 	path = test/resource/chai
 	url = https://github.com/chaijs/chai.git
+	branch = master
 [submodule "test/resource/mocha"]
 	path = test/resource/mocha
 	url = https://github.com/mochajs/mocha.git
+	branch = master
 [submodule "test/resource/chai-as-promised"]
 	path = test/resource/chai-as-promised
 	url = https://github.com/domenic/chai-as-promised.git
+	branch = master

.travis.yml

@@ -1,7 +1,7 @@
 sudo: false
 language: node_js
 node_js:
-    - "node"
+    - "8"
 cache:
     directories:
         - "build"
@@ -10,7 +10,6 @@ env:
     global:
         secure: "NxvkbZ7/Op7BTGQRR3C4q8lLoO29f8WtyNN27NSH7AO3H0vBr1Vp5xO8gn+H2qHEug5HvM+YrZ/xAkNXaZVbOInmBmKVMxqVvdpKp9JM1Amf+gzsXWQphfySvs6iqzyP6cwU/jspdvX/WSakgU5v7PWXxtUIaKxdANt6Rw7W+Pc="
     matrix:
-        - FX_VERSION="54.0"
         - FX_VERSION="52.0.3"
 matrix:
     fast_finish: true
@@ -26,19 +25,15 @@ install:
     - if [ $FX_VERSION = "52.0.3" ]; then
         wget -O tarball "https://archive.mozilla.org/pub/firefox/tinderbox-builds/mozilla-release-linux64-add-on-devel/1491732920/firefox-52.0.3.en-US.linux-x86_64-add-on-devel.tar.bz2";
       fi
-    - if [ $FX_VERSION = "54.0" ]; then
-        wget -O tarball "https://archive.mozilla.org/pub/firefox/tinderbox-builds/mozilla-release-linux64-add-on-devel/1496944705/firefox-54.0.en-US.linux-x86_64-add-on-devel.tar.bz2";
-      fi
     - tar xf tarball
 before_script:
     - export DISPLAY=:99.0
     - sh -e /etc/init.d/xvfb start
     - npm i
     - npm run build
-    - if [ $FX_VERSION = "54.0" ] &&
-         [ $TRAVIS_REPO_SLUG = "zotero/zotero" ] &&
-         [ $TRAVIS_BRANCH = "master" ] &&
-         [ $TRAVIS_PULL_REQUEST = "false" ]; then
+    - if [[ $TRAVIS_REPO_SLUG = "zotero/zotero" &&
+            ($TRAVIS_BRANCH = "master" || $TRAVIS_BRANCH = *-hotfix) &&
+            $TRAVIS_PULL_REQUEST = "false" ]]; then
         mkdir build-zip;
         cd build;
         zip -r ../build-zip/$TRAVIS_COMMIT.zip *;

CONTRIBUTING.md

@@ -2,9 +2,9 @@
 
 ## Bug Reports and Feature Requests
 
-In order to keep product discussions open to as many people as possible, Zotero does not use GitHub Issues for bug reports or feature requests. Please use the [Zotero Forums](https://forums.zotero.org) to report problems and suggest changes.
+Zotero does not use GitHub Issues for bug reports or feature requests. Please post all such requests to the [Zotero Forums](https://forums.zotero.org), where Zotero developers and many others can help. Keeping product discussions in the Zotero Forums allows the entire Zotero community to participate, including domain experts that can address many questions better than Zotero developers.
 
-For confirmed bugs or agreed-upon changes, new issues will be created in the relevant repositories on GitHub by Zotero developers.
+For confirmed bugs or agreed-upon changes, Zotero developers will create new issues in the relevant repositories.
 
 ## Working with Zotero Code
 

COPYING

@@ -1,8 +1,11 @@
-Zotero is Copyright © 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017
+Zotero is Copyright © 2018 Corporation for Digital Scholarship, 
+Vienna, Virginia, USA http://digitalscholar.org
+
+Copyright © 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017
 Roy Rosenzweig Center for History and New Media, George Mason University,
 Fairfax, Virginia, USA  http://zotero.org
 
-The Roy Rosenzweig Center for History and New Media distributes the Zotero source code
+The Corporation for Digital Scholarship distributes the Zotero source code
 under the GNU Affero General Public License, version 3 (AGPLv3). The full text
 of this license is given below.
 

chrome/content/zotero-platform/mac/integration.css

@@ -14,6 +14,10 @@ body[multiline="true"] {
 	width: 800px;
 }
 
+#quick-format-dialog.progress-bar #quick-format-deck {
+	height: 37px;
+}
+
 #quick-format-search {
 	background: white;
 	-moz-appearance: searchfield;

chrome/content/zotero-platform/mac/itembox.css

@@ -29,4 +29,10 @@ textbox
 {
 	margin: -1px 5px -1px 0;
 	padding: 0;
-}
+}
+
+
+/* BEGIN 2X BLOCK -- DO NOT EDIT MANUALLY -- USE 2XIZE */
+@media (min-resolution: 1.25dppx) {
+	.creator-type-label > image  { list-style-image: url('chrome://zotero/skin/mac/arrow-down@2x.png'); }
+}

chrome/content/zotero-platform/mac/overlay.css

@@ -378,9 +378,7 @@
 #zotero-collections-splitter[state=collapsed] > grippy, #zotero-items-splitter[state=collapsed] > grippy
 {
 	-moz-appearance: none;
-	background-image: url("chrome://zotero/skin/mac/vgrippy.png");
-	background-position: center;
-	background-repeat: no-repeat;
+	background: url(chrome://zotero/skin/mac/vgrippy.png) center/auto 8px no-repeat;
 	width: 8px;
 }
 
@@ -399,9 +397,7 @@
 #zotero-tags-splitter > grippy
 {
 	-moz-appearance: none;
-	background-image: url("chrome://zotero/skin/mac/hgrippy.png");
-	background-position: center;
-	background-repeat: no-repeat;
+	background: url(chrome://zotero/skin/mac/hgrippy.png) center/auto 8px no-repeat;
 	height: 8px;
 }
 
@@ -495,13 +491,15 @@ treechildren::-moz-tree-image {
 
 
 /* BEGIN 2X BLOCK -- DO NOT EDIT MANUALLY -- USE 2XIZE */
-@media (min-resolution: 1.5dppx) {
+@media (min-resolution: 1.25dppx) {
 	.zotero-tb-button,.zotero-tb-button:first-child,.zotero-tb-button:last-child  { background: url("chrome://zotero/skin/mac/menubutton-end@2x.png") right center/auto 24px no-repeat; }
 	.zotero-tb-button > .toolbarbutton-icon  { background: url("chrome://zotero/skin/mac/menubutton-start@2x.png") left center/auto 24px no-repeat; }
 	.zotero-tb-button:-moz-window-inactive > .toolbarbutton-icon  { background: url("chrome://zotero/skin/mac/menubutton-start-inactive-window@2x.png") left center/auto 24px no-repeat; }
 	.zotero-tb-button:-moz-window-inactive,.zotero-tb-button:-moz-window-inactive:first-child,.zotero-tb-button:-moz-window-inactive:last-child  { background: url("chrome://zotero/skin/mac/menubutton-end-inactive-window@2x.png") right center/auto 24px no-repeat; }
 	.zotero-tb-button[open="true"],.zotero-tb-button:not([disabled="true"]):hover:active  { background: url("chrome://zotero/skin/mac/menubutton-end-pressed@2x.png") right center/auto 24px no-repeat; }
 	.zotero-tb-button[open="true"] > .toolbarbutton-icon,.zotero-tb-button:not([disabled="true"]):hover:active > .toolbarbutton-icon  { background: url("chrome://zotero/skin/mac/menubutton-start-pressed@2x.png") left center/auto 24px no-repeat; }
+	#zotero-collections-splitter[state=collapsed] > grippy, #zotero-items-splitter[state=collapsed] > grippy { background: url(chrome://zotero/skin/mac/vgrippy@2x.png) center/auto 8px no-repeat; }
+	#zotero-tags-splitter > grippy { background: url(chrome://zotero/skin/mac/hgrippy@2x.png) center/auto 8px no-repeat; }
 	#zotero-tb-advanced-search { list-style-image: url('chrome://zotero/skin/mac/toolbar-advanced-search@2x.png'); }
 	#zotero-tb-note-add { list-style-image: url('chrome://zotero/skin/mac/toolbar-note-add@2x.png'); }
 }

chrome/content/zotero-platform/unix/overlay.css

@@ -168,8 +168,12 @@ toolbar:not([id="nav-bar"]) #zotero-toolbar-buttons separator {
 	background-color: Highlight;
 }
 
+#zotero-collections-tree treechildren::-moz-tree-row {
+	height: 1.3em;
+}
 
-@media (min-resolution: 1.5dppx) {
+
+@media (min-resolution: 1.25dppx) {
 	#zotero-pane .toolbarbutton-icon {
 		width: 16px;
 	}
@@ -224,8 +228,14 @@ tab {
 #zotero-prefs .numberbox-input-box{
 	-moz-appearance: textfield;
 }
-/* Grippy icon missing anyway */
-#zotero-pane splitter{
-	width: 6px;
+
+#zotero-prefs #noteFontSize {
+	min-width: 3.8em;
 }
 
+#zotero-pane splitter {
+	border: 0;
+	width: 6px;
+	background-color: transparent;
+	background-image: none;
+}

chrome/content/zotero-platform/win/overlay.css

@@ -1,3 +1,18 @@
+:root {
+	--theme-border-color: #cecece;
+}
+
+/* Hide horrible blue effect for menu bar and toolbar */
+#navigator-toolbox {
+	-moz-appearance: none;
+}
+
+#zotero-pane #zotero-toolbar {
+	-moz-appearance: none !important;
+	margin-top: -3px;
+	border-bottom-color: var(--theme-border-color);
+}
+
 /*
  As of Fx36, the built-in styles don't properly handle a menu-button within combined buttons.
  
@@ -176,7 +191,7 @@ toolbar:not([id="nav-bar"]) #zotero-toolbar-buttons separator {
 /* End toolbar buttons */
 
 
-@media (min-resolution: 1.5dppx) {
+@media (min-resolution: 1.25dppx) {
 	#zotero-toolbar .toolbarbutton-icon {
 		width: 16px;
 	}
@@ -221,13 +236,44 @@ toolbar:not([id="nav-bar"]) #zotero-toolbar-buttons separator {
 	padding-left: 2px;
 }
 
-#zotero-toolbar:-moz-system-metric(windows-compositor) {
-	-moz-appearance: none !important;
-	background-image: -moz-linear-gradient(rgba(255, 255, 255, 0.5), rgba(255, 255, 255, 0));
-	background-color: rgb(207, 219, 236) !important;
-	border-width: 0 0 1px 0;
-	border-style: solid;
-	border-color: #818790;
+#zotero-collections-splitter:not([state=collapsed]),
+#zotero-items-splitter:not([state=collapsed]),
+#zotero-tags-splitter:not([state=collapsed]) {
+	border: 0;
+	background-color: transparent;
+	position: relative;
+	/* Positive z-index positions the splitter on top of its siblings and makes
+	it clickable on both sides. */
+	z-index: 1;
+}
+
+#zotero-collections-splitter:not([state=collapsed]),
+#zotero-items-splitter:not([state=collapsed]):not([orient=vertical]),
+#zotero-tags-splitter:not([state=collapsed]) {
+	border-inline-end: 1px solid var(--theme-border-color);
+	min-width: 0;
+	width: 3px;
+	margin-inline-start: -3px;
+}
+
+#zotero-tags-splitter:not([state=collapsed]),
+#zotero-items-splitter:not([state=collapsed])[orient=vertical] {
+	border-block-end: 1px solid var(--theme-border-color);
+	min-height: 0;
+	height: 3px;
+	margin-block-start: -3px;
+}
+
+#zotero-collections-splitter > grippy,
+#zotero-items-splitter > grippy,
+#zotero-tags-splitter > grippy {
+	border: 0;
+}
+
+#zotero-collections-splitter:not([state=collapsed]) > grippy,
+#zotero-items-splitter:not([state=collapsed]) > grippy,
+#zotero-tags-splitter:not([state=collapsed]) > grippy {
+	display: none;
 }
 
 #zotero-collections-tree, #zotero-items-tree, #zotero-view-item {
@@ -242,6 +288,10 @@ toolbar:not([id="nav-bar"]) #zotero-toolbar-buttons separator {
 	-moz-border-left-colors: none;
 }
 
+treechildren::-moz-tree-twisty {
+	padding: 0 4px;
+}
+
 /* Undo tree row spacing change in Fx25 on Windows */
 #zotero-collections-tree treechildren::-moz-tree-row,
 #zotero-items-tree treechildren::-moz-tree-row,
@@ -249,8 +299,8 @@ toolbar:not([id="nav-bar"]) #zotero-toolbar-buttons separator {
 	height: 1.6em;
 }
 
-#zotero-collections-tree {
-	border-width: 0 1px 1px 0;
+tree {
+	border-width: 0;
 }
 
 /* Restore row highlighting on drag over, though I'm not sure how we're losing it to begin with. */
@@ -258,15 +308,31 @@ toolbar:not([id="nav-bar"]) #zotero-toolbar-buttons separator {
 	background-color: Highlight;
 }
 
-#zotero-items-tree {
-	border-width: 0 1px;
+#zotero-tag-selector groupbox {
+	-moz-appearance: none;
+	padding: 0;
+	border: 0;
+}
+
+#tags-box {
+	padding-top: 0.1em;
+	padding-left: 0.05em;
+}
+
+#tags-box button {
+	margin: .04em 0 0 .15em !important;
+}
+
+#zotero-editpane-tabs spacer {
+	border: 0;
 }
 
 #zotero-view-item {
 	padding: 0 !important;
 	-moz-appearance: none;
 	background-color: -moz-field;
-	border-width: 1px 0 0  1px;
+	border-width: 1px 0 0  0;
+	border-color: var(--theme-border-color);
 }
 
 #zotero-view-tabbox > tabs {
@@ -275,10 +341,7 @@ toolbar:not([id="nav-bar"]) #zotero-toolbar-buttons separator {
 
 #zotero-item-pane-groupbox {
 	-moz-appearance: none !important;
-	border-radius: 0;
-	border-width: 0 0 0 1px;
-	border-color: #818790;
-	border-style: solid;
+	border-width: 0;
 }
 
 #zotero-editpane-item-box > scrollbox, #zotero-view-item > tabpanel > vbox, 

chrome/content/zotero-platform/win/tagselector.css

@@ -1,4 +1,3 @@
 button {
 	font-family: Segoe UI, sans-serif;
-	font-size: 1em;
 }

chrome/content/zotero/bibliography.js

@@ -146,31 +146,47 @@ var Zotero_File_Interface_Bibliography = new function() {
 			if(_io.useEndnotes && _io.useEndnotes == 1) document.getElementById("displayAs").selectedIndex = 1;
 			let dialog = document.getElementById("zotero-doc-prefs-dialog");
 			dialog.setAttribute('title', `${Zotero.clientName} - ${dialog.getAttribute('title')}`);
-		}
-		if(document.getElementById("formatUsing")) {
-			if(_io.fieldType == "Bookmark") document.getElementById("formatUsing").selectedIndex = 1;
-			var formatOption = (_io.primaryFieldType == "ReferenceMark" ? "referenceMarks" : "fields");
-			document.getElementById("fields").label =
-				Zotero.getString("integration."+formatOption+".label");
-			document.getElementById("fields-caption").textContent =
-				Zotero.getString("integration."+formatOption+".caption");
-			document.getElementById("fields-file-format-notice").textContent =
-				Zotero.getString("integration."+formatOption+".fileFormatNotice");
-			document.getElementById("bookmarks-file-format-notice").textContent =
-				Zotero.getString("integration.fields.fileFormatNotice");
-		}
-		if(document.getElementById("automaticJournalAbbreviations-checkbox")) {
-			if(_io.automaticJournalAbbreviations === undefined) {
-				_io.automaticJournalAbbreviations = Zotero.Prefs.get("cite.automaticJournalAbbreviations");
+			
+			if (document.getElementById("formatUsing-groupbox")) {
+				if (["Field", "ReferenceMark"].includes(_io.primaryFieldType)) {
+					if(_io.fieldType == "Bookmark") document.getElementById("formatUsing").selectedIndex = 1;
+					var formatOption = (_io.primaryFieldType == "ReferenceMark" ? "referenceMarks" : "fields");
+					document.getElementById("fields").label =
+						Zotero.getString("integration."+formatOption+".label");
+					document.getElementById("fields-caption").textContent =
+						Zotero.getString("integration."+formatOption+".caption");
+					document.getElementById("fields-file-format-notice").textContent =
+						Zotero.getString("integration."+formatOption+".fileFormatNotice");
+					document.getElementById("bookmarks-file-format-notice").textContent =
+						Zotero.getString("integration.fields.fileFormatNotice");
+				} else {
+					document.getElementById("formatUsing-groupbox").style.display = "none";
+					_io.fieldType = _io.primaryFieldType;
+				}
 			}
-			if(_io.automaticJournalAbbreviations) {
-				document.getElementById("automaticJournalAbbreviations-checkbox").checked = true;
+			if(document.getElementById("automaticJournalAbbreviations-checkbox")) {
+				if(_io.automaticJournalAbbreviations === undefined) {
+					_io.automaticJournalAbbreviations = Zotero.Prefs.get("cite.automaticJournalAbbreviations");
+				}
+				if(_io.automaticJournalAbbreviations) {
+					document.getElementById("automaticJournalAbbreviations-checkbox").checked = true;
+				}
+				
+				document.getElementById("automaticCitationUpdates-checkbox").checked = !_io.delayCitationUpdates;
 			}
 		}
 		
 		// set style to false, in case this is cancelled
 		_io.style = false;
 	});
+	
+	this.openHelpLink = function() {
+		var url = "https://www.zotero.org/support/word_processor_plugin_usage";
+		var win = Components.classes["@mozilla.org/appshell/window-mediator;1"]
+						.getService(Components.interfaces.nsIWindowMediator)
+						.getMostRecentWindow("navigator:browser");
+		Zotero.launchURL(url);
+	};
 
 	/*
 	 * Called when locale is changed
@@ -192,22 +208,18 @@ var Zotero_File_Interface_Bibliography = new function() {
 		//
 		// For integrationDocPrefs.xul
 		//
-		
-		// update status of displayAs box based on style class
-		if(document.getElementById("displayAs-groupbox")) {
+		if (isDocPrefs) {
+			// update status of displayAs box based on style class
 			var isNote = selectedStyleObj.class == "note";
-			document.getElementById("displayAs-groupbox").hidden = !isNote;
+			var multipleNotesSupported = _io.supportedNotes.length > 1;
+			document.getElementById("displayAs-groupbox").hidden = !isNote || !multipleNotesSupported;
 			
 			// update status of formatUsing box based on style class
-			if(document.getElementById("formatUsing")) {
-				if(isNote) document.getElementById("formatUsing").selectedIndex = 0;
-				document.getElementById("bookmarks").disabled = isNote;
-				document.getElementById("bookmarks-caption").disabled = isNote;
-			}
-		}
-
-		// update status of displayAs box based on style class
-		if(document.getElementById("automaticJournalAbbreviations-vbox")) {
+			if(isNote) document.getElementById("formatUsing").selectedIndex = 0;
+			document.getElementById("bookmarks").disabled = isNote;
+			document.getElementById("bookmarks-caption").disabled = isNote;
+	
+			// update status of displayAs box based on style class
 			document.getElementById("automaticJournalAbbreviations-vbox").hidden =
 				!selectedStyleObj.usesAbbreviation;
 		}
@@ -266,6 +278,7 @@ var Zotero_File_Interface_Bibliography = new function() {
 			}
 			_io.useEndnotes = document.getElementById("displayAs").selectedIndex;
 			_io.fieldType = (document.getElementById("formatUsing").selectedIndex == 0 ? _io.primaryFieldType : _io.secondaryFieldType);
+			_io.delayCitationUpdates = !document.getElementById("automaticCitationUpdates-checkbox").checked;
 		}
 		
 		// remember style and locale if user selected these explicitly
@@ -283,8 +296,7 @@ var Zotero_File_Interface_Bibliography = new function() {
 		document.documentElement.getButton('cancel').click();
 		var win = Zotero.Utilities.Internal.openPreferences('zotero-prefpane-cite', { tab: 'styles-tab' });
 		if (isDocPrefs) {
-			// TODO: Move activate() code elsewhere
-			Zotero.Integration.activate(win);
+			Zotero.Utilities.Internal.activate(win);
 		}
 	};
 }

chrome/content/zotero/bindings/attachmentbox.xml

@@ -160,12 +160,21 @@
 				<parameter name="event"/>
 				<parameter name="type"/>
 				<parameter name="ids"/>
+				<parameter name="extraData"/>
 				<body><![CDATA[
 					if (event != 'modify' || !this.item || !this.item.id) return;
-					for (let i = 0; i < ids.length; i++) {
-						if (ids[i] != this.item.id) {
+					for (let id of ids) {
+						if (id != this.item.id) {
 							continue;
 						}
+						
+						var noteEditor = this._id('attachment-note-editor')
+						if (extraData && extraData[id]
+								&& extraData[id].noteEditorID == noteEditor.instanceID) {
+							//Zotero.debug("Skipping notification from current attachment note field");
+							continue;
+						}
+						
 						this.refresh();
 						break;
 					}
@@ -230,6 +239,7 @@
 						if (this.displayURL) {
 							var urlSpec = this.item.getField('url');
 							urlField.setAttribute('value', urlSpec);
+							urlField.setAttribute('tooltiptext', urlSpec);
 							urlField.setAttribute('hidden', false);
 							if (this.clickableLink) {
 								 urlField.onclick = function (event) {
@@ -250,10 +260,17 @@
 						if (this.displayAccessed) {
 							this._id("accessed-label").value = Zotero.getString('itemFields.accessDate')
 								+ Zotero.getString('punctuation.colon');
-							this._id("accessed").value = Zotero.Date.sqlToDate(
-									this.item.getField('accessDate'), true
-								).toLocaleString();
-							accessed.hidden = false;
+							let val = this.item.getField('accessDate');
+							if (val) {
+								val = Zotero.Date.sqlToDate(val, true);
+							}
+							if (val) {
+								this._id("accessed").value = val.toLocaleString();
+								accessed.hidden = false;
+							}
+							else {
+								accessed.hidden = true;
+							}
 						}
 						else {
 							accessed.hidden = true;

chrome/content/zotero/bindings/itembox.xml

@@ -313,7 +313,6 @@
 						this.itemTypeMenu.parentNode.hidden = true;
 					}
 					
-					
 					//
 					// Clear and rebuild metadata fields
 					//
@@ -427,7 +426,7 @@
 							// Pull out DOI, in case there's a prefix
 							var doi = Zotero.Utilities.cleanDOI(val);
 							if (doi) {
-								doi = "http://dx.doi.org/" + encodeURIComponent(doi);
+								doi = "https://doi.org/" + encodeURIComponent(doi);
 								label.classList.add("pointer");
 								label.setAttribute("onclick", "ZoteroPane_Local.loadURI('" + doi + "', event)");
 								label.setAttribute("tooltiptext", Zotero.getString('locate.online.tooltip'));
@@ -602,10 +601,11 @@
 					}
 					
 					// Move to next or previous field if (shift-)tab was pressed
-					if (this._lastTabIndex && this._tabDirection)
-					{
-						this._focusNextField(this._dynamicFields, this._lastTabIndex, this._tabDirection == -1);
+					if (this._lastTabIndex && this._lastTabIndex != -1) {
+						this._focusNextField(this._lastTabIndex);
 					}
+					
+					this._refreshed = true;
 				]]>
 				</body>
 			</method>
@@ -1046,6 +1046,10 @@
 						var fields = this.getCreatorFields(row);
 						fields.fieldMode = fieldMode;
 						this.modifyCreator(index, fields);
+						if (this.saveOnEdit) {
+							// See note in transformText()
+							this.blurOpenField().then(() => this.item.saveTx());
+						}
 					}
 				]]>
 				</body>
@@ -1083,12 +1087,17 @@
 			<method name="changeTypeTo">
 				<parameter name="itemTypeID"/>
 				<parameter name="menu"/>
-				<body>
-				<![CDATA[
+				<body><![CDATA[
+				return (async function () {
 					if (itemTypeID == this.item.itemTypeID) {
 						return true;
 					}
 					
+					if (this.saveOnEdit) {
+						await this.blurOpenField();
+						await this.item.saveTx();
+					}
+					
 					var fieldsToDelete = this.item.getFieldsNotInType(itemTypeID, true);
 					
 					// Special cases handled below
@@ -1144,15 +1153,16 @@
 						this.item.setType(itemTypeID);
 						
 						if (this.saveOnEdit) {
-							this.item.saveTx();
+							// See note in transformText()
+							await this.blurOpenField();
+							await this.item.saveTx();
 						}
 						else {
 							this.refresh();
 						}
 						
 						if (this.eventHandlers['itemtypechange'] && this.eventHandlers['itemtypechange'].length) {
-							var self = this;
-							this.eventHandlers['itemtypechange'].forEach(function (f) f.bind(self)());
+							this.eventHandlers['itemtypechange'].forEach(f => f.bind(this)());
 						}
 						
 						return true;
@@ -1164,8 +1174,8 @@
 					}
 					
 					return false;
-				]]>
-				</body>
+				}.bind(this))();
+				]]></body>
 			</method>
 			
 			
@@ -1264,6 +1274,7 @@
 						var valueElement = document.createElement("label");
 					}
 					
+					valueElement.setAttribute('id', `itembox-field-value-${fieldName}`);
 					valueElement.setAttribute('fieldname', fieldName);
 					valueElement.setAttribute('flex', 1);
 					
@@ -1303,7 +1314,10 @@
 								if (date) {
 									// If no time, interpret as local, not UTC
 									if (Zotero.Date.isSQLDate(valueText)) {
-										date = Zotero.Date.sqlToDate(valueText);
+										// Add time to avoid showing previous day if date is in
+										// DST (including the current date at 00:00:00) and we're
+										// in standard time
+										date = Zotero.Date.sqlToDate(valueText + ' 12:00:00');
 										valueText = date.toLocaleDateString();
 									}
 									else {
@@ -1412,11 +1426,26 @@
 			
 			<method name="showEditor">
 				<parameter name="elem"/>
-				<body>
-				<![CDATA[
-					// Blur any active fields
-					if (this._dynamicFields) {
-						this._dynamicFields.focus();
+				<body><![CDATA[
+				return (async function () {
+					Zotero.debug(`Showing editor for ${elem.getAttribute('fieldname')}`);
+					
+					var label = Zotero.getAncestorByTagName(elem, 'row').querySelector('label');
+					var lastTabIndex = this._lastTabIndex = parseInt(elem.getAttribute('ztabindex'));
+					
+					// If a field is open, hide it before selecting the new field, which might
+					// trigger a refresh
+					var activeField = this._dynamicFields.querySelector('textbox');
+					if (activeField) {
+						this._refreshed = false;
+						await this.blurOpenField();
+						this._lastTabIndex = lastTabIndex;
+						// If the box was refreshed, the clicked element is no longer valid,
+						// so just focus by tab index
+						if (this._refreshed) {
+							this._focusNextField(this._lastTabIndex);
+							return;
+						}
 					}
 					
 					// In Firefox 45, when clicking a multiline field such as Extra, the event is
@@ -1425,8 +1454,6 @@
 						elem = elem.parentNode;
 					}
 					
-					Zotero.debug('Showing editor');
-					
 					var fieldName = elem.getAttribute('fieldname');
 					var tabindex = elem.getAttribute('ztabindex');
 					
@@ -1468,6 +1495,7 @@
 					}
 					
 					var t = document.createElement("textbox");
+					t.setAttribute('id', `itembox-field-textbox-${fieldName}`);
 					t.setAttribute('value', value);
 					t.setAttribute('fieldname', fieldName);
 					t.setAttribute('ztabindex', tabindex);
@@ -1524,6 +1552,9 @@
 					var box = elem.parentNode;
 					box.replaceChild(t, elem);
 					
+					// Associate textbox with label
+					label.setAttribute('control', t.getAttribute('id'));
+					
 					// Prevent error when clicking between a changed field
 					// and another -- there's probably a better way
 					if (!t.select) {
@@ -1552,12 +1583,9 @@
 					});
 					t.setAttribute('onkeypress', "return document.getBindingParent(this).handleKeyPress(event)");
 					
-					this._tabDirection = false;
-					this._lastTabIndex = tabindex;
-					
 					return t;
-				]]>
-				</body>
+				}.bind(this))();
+				]]></body>
 			</method>
 			
 			
@@ -1600,8 +1628,8 @@
 							textbox.getAttribute('fieldname').split('-');
 						
 						if (stayFocused) {
-							this._lastTabIndex = parseInt(textbox.getAttribute('ztabindex')) - 1;
-							this._tabDirection = 1;
+							this._lastTabIndex = parseInt(textbox.getAttribute('ztabindex'));
+							this._tabDirection = false;
 						}
 						
 						var creator = Zotero.Creators.get(creatorID);
@@ -1634,11 +1662,13 @@
 						fields[creatorField] = creator[creatorField];
 						fields[otherField] = creator[otherField];
 						
-						this.ignoreBlur = true;
-						this.modifyCreator(creatorIndex, fields)
-						.then(function () {
-							this.ignoreBlur = false;
-						}.bind(this));
+						this.modifyCreator(creatorIndex, fields);
+						if (this.saveOnEdit) {
+							this.ignoreBlur = true;
+							this.item.saveTx().then(() => {
+								this.ignoreBlur = false;
+							});
+						}
 					}
 					
 					// Otherwise let the autocomplete popup handle matters
@@ -1662,7 +1692,6 @@
 								break;
 							}
 							
-							
 							// Prevent blur on containing textbox
 							// DEBUG: what happens if this isn't present?
 							event.preventDefault();
@@ -1674,7 +1703,7 @@
 									Zotero.debug("Value hasn't changed");
 									// If + button is disabled, just focus next creator row
 									if (Zotero.getAncestorByTagName(target, 'row').lastChild.lastChild.disabled) {
-										this._focusNextField(this._dynamicFields, this._lastTabIndex, false);
+										this._focusNextField(this._lastTabIndex);
 									}
 									else {
 										var creatorFields = this.getCreatorFields(Zotero.getAncestorByTagName(target, 'row'));
@@ -1714,10 +1743,12 @@
 							return false;
 							
 						case event.DOM_VK_TAB:
-							this._tabDirection = event.shiftKey ? -1 : 1;
-							// Blur the old manually -- not sure why this is necessary,
-							// but it prevents an immediate blur() on the next tag
-							focused.blur();
+							if (event.shiftKey) {
+								this._focusNextField(this._lastTabIndex, true);
+							}
+							else {
+								this._focusNextField(++this._lastTabIndex);
+							}
 							return false;
 					}
 					
@@ -1747,8 +1778,11 @@
 			<method name="hideEditor">
 				<parameter name="textbox"/>
 				<body><![CDATA[
-				return Zotero.spawn(function* () {
-					Zotero.debug('Hiding editor');
+				return (async function () {
+					Zotero.debug(`Hiding editor for ${textbox.getAttribute('fieldname')}`);
+					
+					var label = Zotero.getAncestorByTagName(textbox, 'row').querySelector('label');
+					this._lastTabIndex = -1;
 					
 					// Prevent autocomplete breakage in Firefox 3
 					if (textbox.mController) {
@@ -1763,6 +1797,7 @@
 					
 					var elem;
 					var [field, creatorIndex, creatorField] = fieldName.split('-');
+					var newVal;
 					
 					// Creator fields
 					if (field == 'creator') {
@@ -1793,7 +1828,7 @@
 							if (creatorsToShift > 0) { 
 								//Add extra creators
 								for (var i=0;i<nameArray.length;i++) {
-									yield this.modifyCreator(i + initNumCreators, otherFields, true);
+									this.modifyCreator(i + initNumCreators, otherFields);
 								}
 								
 								//Shift existing creators
@@ -1815,7 +1850,7 @@
 									otherFields.lastName=tempName;
 									otherFields.firstName='';
 								}
-								yield this.modifyCreator(creatorIndex, otherFields, true);
+								this.modifyCreator(creatorIndex, otherFields);
 								creatorIndex++;
 							}
 							this._tabDirection = tabDirectionBuffer;
@@ -1828,11 +1863,7 @@
 							}
 						}
 						else {
-							yield this.modifyCreator(creatorIndex, otherFields);
-						}
-						
-						if (this.saveOnEdit) {
-							yield this.item.saveTx();
+							this.modifyCreator(creatorIndex, otherFields);
 						}
 						
 						var val = this.item.getCreator(creatorIndex);
@@ -1849,7 +1880,17 @@
 							}
 						}
 						
-						var newVal = val;
+						newVal = val;
+						
+						// Reset creator mode settings here so that flex attribute gets reset
+						this.switchCreatorMode(row, (otherFields.fieldMode ? 1 : 0), true);
+						if (Zotero.ItemTypes.getName(this.item.itemTypeID) === "bookSection") {
+							var creatorTypeLabels = document.getAnonymousNodes(this)[0].getElementsByClassName("creator-type-label");
+							Zotero.debug(creatorTypeLabels[creatorTypeLabels.length-1] + "");
+							document.getElementById("zotero-author-guidance").show({
+								forEl: creatorTypeLabels[creatorTypeLabels.length-1]
+							});
+						}
 					}
 					
 					// Fields
@@ -1858,8 +1899,12 @@
 						if (value != '') {
 							switch (fieldName) {
 								case 'accessDate':
+									// Allow "now" to use current time
+									if (value == 'now') {
+										value = Zotero.Date.dateToSQL(new Date(), true);
+									}
 									// If just date, don't convert to UTC
-									if (Zotero.Date.isSQLDate(value)) {
+									else if (Zotero.Date.isSQLDate(value)) {
 										var localDate = Zotero.Date.sqlToDate(value);
 										value = Zotero.Date.dateToSQL(localDate).replace(' 00:00:00', '');
 									}
@@ -1914,40 +1959,26 @@
 							}
 						}
 						
-						yield this._modifyField(fieldName, value, this.saveOnEdit);
-						
-						var newVal = this.item.getField(fieldName);
+						this._modifyField(fieldName, value);
+						newVal = this.item.getField(fieldName);
 					}
 					
-					// If box is still open (due to field not being modified and there not being
-					// a refresh), close it manually
-					if (textbox && textbox.parentNode) {
-						elem = this.createValueElement(
-							newVal,
-							fieldName,
-							tabindex
-						);
-						var box = textbox.parentNode;
-						box.replaceChild(elem,textbox);
-					}
+					// Close box
+					elem = this.createValueElement(
+						newVal,
+						fieldName,
+						tabindex
+					);
+					var box = textbox.parentNode;
+					box.replaceChild(elem, textbox);
 					
-					if(field === 'creator') {
-						// Reset creator mode settings here so that flex attribute gets reset
-						this.switchCreatorMode(row, (otherFields.fieldMode ? 1 : 0), true);
-						if(Zotero.ItemTypes.getName(this.item.itemTypeID) === "bookSection") {
-							var creatorTypeLabels = document.getAnonymousNodes(this)[0].getElementsByClassName("creator-type-label");
-							Zotero.debug(creatorTypeLabels[creatorTypeLabels.length-1] + "");
-							document.getElementById("zotero-author-guidance").show({
-								forEl: creatorTypeLabels[creatorTypeLabels.length-1]
-							});
-						}
-					}
+					// Disassociate textbox from label
+					label.setAttribute('control', elem.getAttribute('id'));
 					
-					if (this._tabDirection) {
-						var focusBox = this._dynamicFields;
-						this._focusNextField(focusBox, this._lastTabIndex, this._tabDirection == -1);
+					if (this.saveOnEdit) {
+						await this.item.saveTx();
 					}
-				}, this);
+				}.bind(this))();
 				]]></body>
 			</method>
 			
@@ -1978,14 +2009,8 @@
 			<method name="_modifyField">
 				<parameter name="field"/>
 				<parameter name="value"/>
-				<parameter name="save"/>
 				<body><![CDATA[
-					return Zotero.spawn(function* () {
-						this.item.setField(field, value);
-						if (save) {
-							yield this.item.saveTx();
-						}
-					}, this);
+					this.item.setField(field, value);
 				]]></body>
 			</method>
 			
@@ -2022,7 +2047,7 @@
 				<parameter name="label"/>
 				<parameter name="mode"/>
 				<body><![CDATA[
-					return Zotero.spawn(function* () {
+					return (async function () {
 						var val = this._getFieldValue(label);
 						switch (mode) {
 							case 'title':
@@ -2040,12 +2065,14 @@
 								throw ("Invalid transform mode '" + mode + "' in zoteroitembox.textTransform()");
 						}
 						this._setFieldValue(label, newVal);
+						this._modifyField(label.getAttribute('fieldname'), newVal);
 						if (this.saveOnEdit) {
-							// See note in modifyCreator()
-							yield this.blurOpenField();
+							// If a field is open, blur it, which will trigger a save and cause
+							// the saveTx() to be a no-op
+							await this.blurOpenField();
+							await this.item.saveTx();
 						}
-						return this._modifyField(label.getAttribute('fieldname'), newVal, this.saveOnEdit);
-					}, this);
+					}.bind(this))();
 				]]></body>
 			</method>
 			
@@ -2085,9 +2112,7 @@
 			<method name="modifyCreator">
 				<parameter name="index"/>
 				<parameter name="fields"/>
-				<parameter name="skipSave"/>
 				<body><![CDATA[
-				return Zotero.spawn(function* () {
 					var libraryID = this.item.libraryID;
 					var firstName = fields.firstName;
 					var lastName = fields.lastName;
@@ -2099,28 +2124,12 @@
 					// Don't save empty creators
 					if (!firstName && !lastName){
 						if (!oldCreator) {
-							return;
+							return false;
 						}
-						this.item.removeCreator(index);
-						if (this.saveOnEdit && !skipSave) {
-							// Make sure any open field is saved, since a blur() isn't otherwise
-							// triggered clicking directly to a popup menu. (If a field is open, the
-							// saveTx() below will become a no-op.)
-							yield this.blurOpenField();
-							
-							return this.item.saveTx();
-						}
-						return;
+						return this.item.removeCreator(index);
 					}
 					
-					var changed = this.item.setCreator(index, fields);
-					if (changed && this.saveOnEdit && !skipSave) {
-						// See note above
-						yield this.blurOpenField();
-						
-						return this.item.saveTx();
-					}
-				}, this);
+					return this.item.setCreator(index, fields);
 				]]></body>
 			</method>
 			
@@ -2131,7 +2140,7 @@
 			<method name="swapNames">
 				<parameter name="event"/>
 				<body><![CDATA[
-				return Zotero.Promise.try(function () {
+				return (async function () {
 					var row = Zotero.getAncestorByTagName(document.popupNode, 'row');
 					var typeBox = row.getElementsByAttribute('popup', 'creator-type-menu')[0];
 					var creatorIndex = parseInt(typeBox.getAttribute('fieldname').split('-')[1]);
@@ -2140,8 +2149,13 @@
 					var firstName = fields.firstName;
 					fields.lastName = firstName;
 					fields.firstName = lastName;
-					return this.modifyCreator(creatorIndex, fields);
-				}.bind(this));
+					this.modifyCreator(creatorIndex, fields);
+					if (this.saveOnEdit) {
+						// See note in transformText()
+						await this.blurOpenField();
+						await this.item.saveTx();
+					}
+				}.bind(this))();
 				]]></body>
 			</method>
 			
@@ -2168,9 +2182,8 @@
 					this.item.setCreator(newIndex, a);
 					this.item.setCreator(index, b);
 					if (this.saveOnEdit) {
-						// See note in modifyCreator()
+						// See note in transformText()
 						yield this.blurOpenField();
-						
 						return this.item.saveTx();
 					}
 				}, this);
@@ -2200,7 +2213,7 @@
 			<method name="focusFirstField">
 				<body>
 				<![CDATA[
-					this._focusNextField(this._dynamicFields, 0, false);
+					this._focusNextField(1);
 				]]>
 				</body>
 			</method>
@@ -2215,11 +2228,11 @@
 				completes, so it doesn't know where it's supposed to go next.)
 			-->
 			<method name="_focusNextField">
-				<parameter name="box"/>
 				<parameter name="tabindex"/>
 				<parameter name="back"/>
 				<body>
 				<![CDATA[
+					var box = this._dynamicFields;
 					tabindex = parseInt(tabindex);
 					
 					// Get all fields with ztabindex attributes
@@ -2241,9 +2254,9 @@
 						}
 					}
 					else {
-						Zotero.debug('Looking for next tabindex after ' + tabindex, 4);
+						Zotero.debug('Looking for tabindex ' + tabindex, 4);
 						for (var pos = 0; pos < tabbableFields.length; pos++) {
-							if (parseInt(tabbableFields[pos].getAttribute('ztabindex')) > tabindex) {
+							if (parseInt(tabbableFields[pos].getAttribute('ztabindex')) >= tabindex) {
 								next = tabbableFields[pos];
 								break;
 							}
@@ -2278,12 +2291,13 @@
 			
 			<method name="blurOpenField">
 				<body><![CDATA[
-					return Zotero.spawn(function* () {
-						var textboxes = document.getAnonymousNodes(this)[0].getElementsByTagName('textbox');
-						if (textboxes && textboxes.length) {
-							yield this.blurHandler(textboxes[0]);
+					return (async function () {
+						var activeField = this._dynamicFields.querySelector('textbox');
+						if (!activeField) {
+							return false;
 						}
-					}, this);
+						return this.blurHandler(activeField);
+					}.bind(this))();
 				]]></body>
 			</method>
 			
@@ -2385,7 +2399,11 @@
 							};
 							itemBox._updateAutoCompleteParams(row, changedParams);
 							
-							itemBox.modifyCreator(index, fields);"/>
+							itemBox.modifyCreator(index, fields);
+							if (itemBox.saveOnEdit) {
+								itemBox.item.saveTx();
+							}
+							"/>
 					<menupopup id="zotero-field-transform-menu">
 						<menu label="&zotero.item.textTransform;">
 							<menupopup>

chrome/content/zotero/bindings/noteeditor.xml

@@ -149,7 +149,7 @@
 			
 			<constructor>
 			<![CDATA[
-				this._instanceID = Zotero.Utilities.randomString();
+				this.instanceID = Zotero.Utilities.randomString();
 				this._notifierID = Zotero.Notifier.registerObserver(this, ['item'], 'noteeditor');
 			]]>
 			</constructor>
@@ -172,7 +172,7 @@
 						if (id != this.item.id) {
 							continue;
 						}
-						if (extraData && extraData[id] && extraData[id].noteEditorID == this._instanceID) {
+						if (extraData && extraData[id] && extraData[id].noteEditorID == this.instanceID) {
 							//Zotero.debug("Skipping notification from current note field");
 							continue;
 						}
@@ -275,7 +275,7 @@
 									this.noteField.changed = false;
 									yield this.item.saveTx({
 										notifierData: {
-											noteEditorID: this._instanceID
+											noteEditorID: this.instanceID
 										}
 									});
 								}

chrome/content/zotero/bindings/relatedbox.xml

@@ -152,28 +152,7 @@
 							let id = relatedItem.id;
 							let icon = document.createElement("image");
 							icon.className = "zotero-box-icon";
-							let type = Zotero.ItemTypes.getName(relatedItem.itemTypeID);
-							if (type=='attachment')
-							{
-								switch (relatedItem.attaachmentLinkMode) {
-									case Zotero.Attachments.LINK_MODE_LINKED_URL:
-										type += '-web-link';
-										break;
-									
-									case Zotero.Attachments.LINK_MODE_IMPORTED_URL:
-										type += '-snapshot';
-										break;
-									
-									case Zotero.Attachments.LINK_MODE_LINKED_FILE:
-										type += '-link';
-										break;
-									
-									case Zotero.Attachments.LINK_MODE_IMPORTED_FILE:
-										type += '-file';
-										break;
-								}
-							}
-							icon.setAttribute('src','chrome://zotero/skin/treeitem-' + type + '.png');
+							icon.setAttribute('src', relatedItem.getImageSrc());
 					
 							var label = document.createElement("label");
 							label.className = "zotero-box-label";

chrome/content/zotero/bindings/styled-textbox.xml

@@ -410,15 +410,6 @@
 								}
 								switch (event.type) {
 									case 'keydown':
-										// Intercept and manually trigger redo for Cmd-Shift-Z,
-										// which keeps it from toggling the Zotero pane instead
-										if (Zotero.isMac && event.metaKey && event.shiftKey && !event.ctrlKey
-												&& !event.altKey && event.keyCode == 90) {
-											event.stopPropagation();
-											event.preventDefault();
-											this.redo();
-											return;
-										}
 										// Handle forward-delete, which doesn't register as a keypress
 										// when a selection is cleared
 										if (event.which == event.DOM_VK_DELETE) {
@@ -609,19 +600,12 @@
 				</body>
 			</method>
 			
-			<method name="redo">
-				<body>
-				<![CDATA[
-					this._editor.undoManager.redo();
-				]]>
-				</body>
-			</method>
-			
 			<method name="clearUndo">
 				<body>
 				<![CDATA[
 					if (this._editor) {
 						this._editor.undoManager.clear();
+						this._editor.undoManager.add();
 					}
 				]]>
 				</body>
@@ -707,10 +691,16 @@
 								}
 								if (self._value) {
 									self.value = self._value;
+									
+									// Prevent undoing to empty note after initialization
+									self._editor.undoManager.clear();
+									self._editor.undoManager.add();
 								}
 								if (self._focus) {
-									self._iframe.focus();
-									self._editor.focus();
+									setTimeout(function () {
+										self._iframe.focus();
+										self._editor.focus();
+									});
 									self._focus = false;
 								}
 								

chrome/content/zotero/bindings/zoterosearch.xml

@@ -49,7 +49,16 @@
 					<![CDATA[
 						this.searchRef = val;
 						
-						this.buildLibraryMenu();
+						var libraryMenu = this.id('libraryMenu');
+						var libraries = Zotero.Libraries.getAll();
+						Zotero.Utilities.Internal.buildLibraryMenu(
+							libraryMenu, libraries, this.searchRef.libraryID
+						);
+						if (this.searchRef.id) {
+							libraryMenu.disabled = true;
+						}
+						this.updateLibrary();
+						
 						
 						var conditionsBox = this.id('conditions');
 						while(conditionsBox.hasChildNodes())
@@ -81,43 +90,6 @@
 				</setter>
 			</property>
 			
-			<method name="buildLibraryMenu">
-				<body><![CDATA[
-					var menulist = this.id('libraryMenu');
-					var menupopup = menulist.firstChild;
-					
-					while (menupopup.hasChildNodes()) {
-						menupopup.removeChild(menupopup.firstChild);
-					}
-					
-					var libraryID = this.searchRef.libraryID;
-					var libraryIndex = 0;
-					
-					var libraries = Zotero.Libraries.getAll();
-					var selectedIndex = 0;
-					var i = 0;
-					for (let library of libraries) {
-						let menuitem = document.createElement('menuitem');
-						menuitem.setAttribute('label', library.name);
-						menuitem.setAttribute('libraryID', library.libraryID);
-						menupopup.appendChild(menuitem);
-						if (library.libraryID == libraryID) {
-							selectedIndex = i;
-						}
-						i++
-					}
-					
-					menulist.appendChild(menupopup);
-					menulist.selectedIndex = selectedIndex;
-					
-					if (this.searchRef.id) {
-						this.id('libraryMenu').disabled = true;
-					}
-					
-					this.updateLibrary();
-				]]></body>
-			</method>
-			
 			<method name="addCondition">
 				<parameter name="ref"/>
 				<body>
@@ -170,7 +142,7 @@
 			<method name="updateLibrary">
 				<body><![CDATA[
 					var menu = this.id('libraryMenu');
-					var libraryID = parseInt(menu.selectedItem.getAttribute('libraryID'));
+					var libraryID = parseInt(menu.selectedItem.value);
 					
 				 	if (this.onLibraryChange) {
 				 		this.onLibraryChange(libraryID);
@@ -437,6 +409,7 @@
 				case 'dateModified':
 				case 'itemType':
 				case 'fileTypeID':
+				case 'publicationTitle':
 				case 'tag':
 				case 'note':
 				case 'childNote':

chrome/content/zotero/downloadOverlay.js

@@ -125,8 +125,7 @@ var Zotero_DownloadOverlay = new function() {
 				try {
 				if (item && item.getFile()) {
 					timer.cancel();
-					var recognizer = new win.Zotero_RecognizePDF.ItemRecognizer();
-					recognizer.recognizeItems([item]);
+					Zotero.RecognizePDF.recognizeItems([item]);
 				}
 				} catch(e) { dump(e.toSource()) };
 			}, 1000, Components.interfaces.nsITimer.TYPE_REPEATING_SLACK);
@@ -145,15 +144,7 @@ var Zotero_DownloadOverlay = new function() {
 		// to happen automatically
 		if(zoteroSelected) document.getElementById('rememberChoice').selected = false;
 		document.getElementById('rememberChoice').disabled = zoteroSelected;
-		
-		// disable recognizePDF checkbox as necessary
-		if(!Zotero.Fulltext.pdfConverterIsRegistered()) {
-			document.getElementById('zotero-noPDFTools-description').hidden = !zoteroSelected;
-			document.getElementById('zotero-recognizePDF').disabled = true;
-			window.sizeToContent();
-		} else {
-			document.getElementById('zotero-recognizePDF').disabled = !zoteroSelected;
-		}
+		document.getElementById('zotero-recognizePDF').disabled = !zoteroSelected;
 		
 		Zotero_DownloadOverlay.updateLibraryNote();
 	};
@@ -212,9 +203,6 @@ var Zotero_DownloadOverlay = new function() {
 			recognizePDF.label = Zotero.getString("pane.items.menu.recognizePDF");
 			recognizePDF.hidden = false;
 			recognizePDF.disabled = true;
-			if(!Zotero.Fulltext.pdfConverterIsRegistered()) {
-				recognizePDF.checked = false;
-			}
 		}
 	};
 }

chrome/content/zotero/downloadOverlay.xul

@@ -43,7 +43,6 @@
 			<vbox style="margin-left: 15px">
 				<description id="zotero-saveToLibrary-description" style="font: small-caption; font-weight: normal" hidden="true">&zotero.downloadManager.saveToLibrary.description;</description>
 				<checkbox id="zotero-recognizePDF" hidden="true" persist="checked" disabled="true"/>
-				<description style="margin-left: 20px; font: small-caption; font-weight: normal" id="zotero-noPDFTools-description" hidden="true">&zotero.downloadManager.noPDFTools.description;</description>
 			</vbox>
 		</vbox>
 	</radiogroup>

chrome/content/zotero/fileInterface.js

@@ -23,6 +23,8 @@
     ***** END LICENSE BLOCK *****
 */
 
+Components.utils.import("resource://gre/modules/osfile.jsm")
+
 /****Zotero_File_Exporter****
  **
  * A class to handle exporting of items, collections, or the entire library
@@ -206,13 +208,119 @@ var Zotero_File_Interface = new function() {
 		}
 	}
 	
+	
+	this.getMendeleyDirectory = function () {
+		Components.classes["@mozilla.org/net/osfileconstantsservice;1"]
+			.getService(Components.interfaces.nsIOSFileConstantsService)
+			.init();
+		var path = OS.Constants.Path.homeDir;
+		if (Zotero.isMac) {
+			path = OS.Path.join(path, 'Library', 'Application Support', 'Mendeley Desktop');
+		}
+		else if (Zotero.isWin) {
+			path = OS.Path.join(path, 'AppData', 'Local', 'Mendeley Ltd', 'Mendeley Desktop');
+		}
+		else if (Zotero.isLinux) {
+			path = OS.Path.join(path, '.local', 'share', 'data', 'Mendeley Ltd.', 'Mendeley Desktop');
+		}
+		else {
+			throw new Error("Invalid platform");
+		}
+		return path;
+	};
+	
+	
+	this.findMendeleyDatabases = async function () {
+		var dbs = [];
+		try {
+			var dir = this.getMendeleyDirectory();
+			if (!await OS.File.exists(dir)) {
+				Zotero.debug(`${dir} does not exist`);
+				return dbs;
+			}
+			await Zotero.File.iterateDirectory(dir, function* (iterator) {
+				while (true) {
+					let entry = yield iterator.next();
+					if (entry.isDir) continue;
+					// online.sqlite, counterintuitively, is the default database before you sign in
+					if (entry.name == 'online.sqlite' || entry.name.endsWith('@www.mendeley.com.sqlite')) {
+						dbs.push({
+							name: entry.name,
+							path: entry.path,
+							lastModified: null,
+							size: null
+						});
+					}
+				}
+			});
+			for (let i = 0; i < dbs.length; i++) {
+				let dbPath = OS.Path.join(dir, dbs[i].name);
+				let info = await OS.File.stat(dbPath);
+				dbs[i].size = info.size;
+				dbs[i].lastModified = info.lastModificationDate;
+			}
+			dbs.sort((a, b) => {
+				return b.lastModified - a.lastModified;
+			});
+		}
+		catch (e) {
+			Zotero.logError(e);
+		}
+		return dbs;
+	};
+	
+	
+	this.showImportWizard = function () {
+		var libraryID = Zotero.Libraries.userLibraryID;
+		try {
+			let zp = Zotero.getActiveZoteroPane();
+			libraryID = zp.getSelectedLibraryID();
+		}
+		catch (e) {
+			Zotero.logError(e);
+		}
+		var args = {
+			libraryID
+		};
+		args.wrappedJSObject = args;
+		
+		Services.ww.openWindow(null, "chrome://zotero/content/import/importWizard.xul",
+			"importFile", "chrome,dialog=yes,centerscreen,width=600,height=400", args);
+	};
+	
+	
 	/**
 	 * Creates Zotero.Translate instance and shows file picker for file import
+	 *
+	 * @param {Object} options
+	 * @param {nsIFile|string|null} [options.file=null] - File to import, or none to show a filepicker
+	 * @param {Boolean} [options.addToLibraryRoot=false]
+	 * @param {Boolean} [options.createNewCollection=true] - Put items in a new collection
+	 * @param {Function} [options.onBeforeImport] - Callback to receive translation object, useful
+	 *     for displaying progress in a different way. This also causes an error to be throw
+	 *     instead of shown in the main window.
 	 */
-	this.importFile = Zotero.Promise.coroutine(function* (file, createNewCollection) {
-		if(createNewCollection === undefined) {
+	this.importFile = Zotero.Promise.coroutine(function* (options = {}) {
+		if (!options) {
+			options = {};
+		}
+		if (typeof options == 'string' || options instanceof Components.interfaces.nsIFile) {
+			Zotero.debug("WARNING: importFile() now takes a single options object -- update your code");
+			options = {
+				file: options,
+				createNewCollection: arguments[1]
+			};
+		}
+		
+		var file = options.file ? Zotero.File.pathToFile(options.file) : null;
+		var createNewCollection = options.createNewCollection;
+		var addToLibraryRoot = options.addToLibraryRoot;
+		var onBeforeImport = options.onBeforeImport;
+		
+		if (createNewCollection === undefined && !addToLibraryRoot) {
 			createNewCollection = true;
-		} else if(!createNewCollection) {
+		}
+		else if (!createNewCollection) {
 			try {
 				if (!ZoteroPane.collectionsView.editable) {
 					ZoteroPane.collectionsView.selectLibrary(null);
@@ -220,32 +328,40 @@ var Zotero_File_Interface = new function() {
 			} catch(e) {}
 		}
 		
-		var translation = new Zotero.Translate.Import();
-		if (!file) {
-			let translators = yield translation.getTranslators();
-			const nsIFilePicker = Components.interfaces.nsIFilePicker;
-			var fp = Components.classes["@mozilla.org/filepicker;1"]
-					.createInstance(nsIFilePicker);
-			fp.init(window, Zotero.getString("fileInterface.import"), nsIFilePicker.modeOpen);
-			
-			fp.appendFilters(nsIFilePicker.filterAll);
-			
-			var collation = Zotero.getLocaleCollation();
-			translators.sort((a, b) => collation.compareString(1, a.label, b.label))
-			for (let translator of translators) {
-				fp.appendFilter(translator.label, "*." + translator.target);
-			}
-			
-			var rv = fp.show();
-			if (rv !== nsIFilePicker.returnOK && rv !== nsIFilePicker.returnReplace) {
-				return false;
-			}
-			
-			file = fp.file;
+		var defaultNewCollectionPrefix = Zotero.getString("fileInterface.imported");
+		
+		var translation;
+		// Check if the file is an SQLite database
+		var sample = yield Zotero.File.getSample(file.path);
+		if (file.path == Zotero.DataDirectory.getDatabase()) {
+			// Blacklist the current Zotero database, which would cause a hang
+		}
+		else if (Zotero.MIME.sniffForMIMEType(sample) == 'application/x-sqlite3') {
+			// Mendeley import doesn't use the real translation architecture, but we create a
+			// translation object with the same interface
+			translation = yield _getMendeleyTranslation();
+			translation.createNewCollection = createNewCollection;
+			defaultNewCollectionPrefix = Zotero.getString(
+				'fileInterface.appImportCollection', 'Mendeley'
+			);
+		}
+		else if (file.path.endsWith('@www.mendeley.com.sqlite')
+				|| file.path.endsWith('online.sqlite')) {
+			// Keep in sync with importWizard.js
+			throw new Error('Encrypted Mendeley database');
+		}
+		
+		if (!translation) {
+			translation = new Zotero.Translate.Import();
 		}
-
 		translation.setLocation(file);
-		yield _finishImport(translation, createNewCollection);
+		return _finishImport({
+			translation,
+			createNewCollection,
+			addToLibraryRoot,
+			defaultNewCollectionPrefix,
+			onBeforeImport
+		});
 	});
 	
 	
@@ -273,7 +389,10 @@ var Zotero_File_Interface = new function() {
 			}
 		} catch(e) {}
 		
-		yield _finishImport(translation, false);
+		yield _finishImport({
+			translation,
+			createNewCollection: false
+		});
 		
 		// Select imported items
 		try {
@@ -287,17 +406,36 @@ var Zotero_File_Interface = new function() {
 	});
 	
 	
-	var _finishImport = Zotero.Promise.coroutine(function* (translation, createNewCollection) {
+	var _finishImport = Zotero.Promise.coroutine(function* (options) {
+		var t = performance.now();
+		
+		var translation = options.translation;
+		var addToLibraryRoot = options.addToLibraryRoot;
+		var createNewCollection = options.createNewCollection;
+		var defaultNewCollectionPrefix = options.defaultNewCollectionPrefix;
+		var onBeforeImport = options.onBeforeImport;
+		
+		if (addToLibraryRoot && createNewCollection) {
+			throw new Error("Can't add to library root and create new collection");
+		}
+		
+		var showProgressWindow = !onBeforeImport;
+		
 		let translators = yield translation.getTranslators();
-
-		if(!translators.length) {
-			var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
-									.getService(Components.interfaces.nsIPromptService);
-			var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_OK)
-								+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_IS_STRING);
-			var index = ps.confirmEx(
+		
+		// Unrecognized file
+		if (!translators.length) {
+			if (onBeforeImport) {
+				yield onBeforeImport(false);
+			}
+			
+			let ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
+				.getService(Components.interfaces.nsIPromptService);
+			let buttonFlags = ps.BUTTON_POS_0 * ps.BUTTON_TITLE_OK
+				+ ps.BUTTON_POS_1 * ps.BUTTON_TITLE_IS_STRING;
+			let index = ps.confirmEx(
 				null,
-				"",
+				Zotero.getString('general.error'),
 				Zotero.getString("fileInterface.unsupportedFormat"),
 				buttonFlags,
 				null,
@@ -305,17 +443,27 @@ var Zotero_File_Interface = new function() {
 				null, null, {}
 			);
 			if (index == 1) {
-				ZoteroPane_Local.loadURI("http://zotero.org/support/kb/importing");
+				Zotero.launchURL("https://www.zotero.org/support/kb/importing");
 			}
-			return;
+			return false;
 		}
-
-		let importCollection = null, libraryID = Zotero.Libraries.userLibraryID;
+		
+		var libraryID = Zotero.Libraries.userLibraryID;
+		var importCollection = null;
 		try {
-			libraryID = ZoteroPane.getSelectedLibraryID();
-			importCollection = ZoteroPane.getSelectedCollection();
-		} catch(e) {}
-
+			let zp = Zotero.getActiveZoteroPane();
+			libraryID = zp.getSelectedLibraryID();
+			if (addToLibraryRoot) {
+				yield zp.collectionsView.selectLibrary(libraryID);
+			}
+			else if (!createNewCollection) {
+				importCollection = zp.getSelectedCollection();
+			}
+		}
+		catch (e) {
+			Zotero.logError(e);
+		}
+		
 		if(createNewCollection) {
 			// Create a new collection to take imported items
 			let collectionName;
@@ -330,8 +478,9 @@ var Zotero_File_Interface = new function() {
 						break;
 					}
 				}
-			} else {
-				collectionName = Zotero.getString("fileInterface.imported")+" "+(new Date()).toLocaleString();
+			}
+			else {
+				collectionName = defaultNewCollectionPrefix + " " + (new Date()).toLocaleString();
 			}
 			importCollection = new Zotero.Collection;
 			importCollection.libraryID = libraryID;
@@ -342,22 +491,29 @@ var Zotero_File_Interface = new function() {
 		translation.setTranslator(translators[0]);
 		
 		// Show progress popup
-		var progressWin = new Zotero.ProgressWindow({
-			closeOnClick: false
-		});
-		progressWin.changeHeadline(Zotero.getString('fileInterface.importing'));
-		var icon = 'chrome://zotero/skin/treesource-unfiled' + (Zotero.hiDPI ? "@2x" : "") + '.png';
-		let progress = new progressWin.ItemProgress(
-			icon, translation.path ? OS.Path.basename(translation.path) : translators[0].label
-		);
-		progressWin.show();
+		var progressWin;
+		var progress;
+		if (showProgressWindow) {
+			progressWin = new Zotero.ProgressWindow({
+				closeOnClick: false
+			});
+			progressWin.changeHeadline(Zotero.getString('fileInterface.importing'));
+			let icon = 'chrome://zotero/skin/treesource-unfiled' + (Zotero.hiDPI ? "@2x" : "") + '.png';
+			progress = new progressWin.ItemProgress(
+				icon, translation.path ? OS.Path.basename(translation.path) : translators[0].label
+			);
+			progressWin.show();
+			
+			translation.setHandler("itemDone",  function () {
+				progress.setProgress(translation.getProgress());
+			});
+			
+			yield Zotero.Promise.delay(0);
+		}
+		else {
+			yield onBeforeImport(translation);
+		}
 		
-		translation.setHandler("itemDone",  function () {
-			progress.setProgress(translation.getProgress());
-		});
-
-		yield Zotero.Promise.delay(0);
-
 		let failed = false;
 		try {
 			yield translation.translate({
@@ -365,6 +521,10 @@ var Zotero_File_Interface = new function() {
 				collections: importCollection ? [importCollection.id] : null
 			});
 		} catch(e) {
+			if (!showProgressWindow) {
+				throw e;
+			}
+			
 			progressWin.close();
 			Zotero.logError(e);
 			Zotero.alert(
@@ -372,26 +532,62 @@ var Zotero_File_Interface = new function() {
 				Zotero.getString('general.error'),
 				Zotero.getString("fileInterface.importError")
 			);
-			return;
+			return false;
 		}
 		
-		// Show popup on completion
 		var numItems = translation.newItems.length;
-		progressWin.changeHeadline(Zotero.getString('fileInterface.importComplete'));
-		if (numItems == 1) {
-			var icon = translation.newItems[0].getImageSrc();
+		
+		// Show popup on completion
+		if (showProgressWindow) {
+			progressWin.changeHeadline(Zotero.getString('fileInterface.importComplete'));
+			let icon;
+			if (numItems == 1) {
+				icon = translation.newItems[0].getImageSrc();
+			}
+			else {
+				icon = 'chrome://zotero/skin/treesource-unfiled' + (Zotero.hiDPI ? "@2x" : "") + '.png';
+			}
+			let text = Zotero.getString(`fileInterface.itemsWereImported`, numItems, numItems);
+			progress.setIcon(icon);
+			progress.setText(text);
+			// For synchronous translators, which don't update progress
+			progress.setProgress(100);
+			progressWin.startCloseTimer(5000);
 		}
-		else {
-			var icon = 'chrome://zotero/skin/treesource-unfiled' + (Zotero.hiDPI ? "@2x" : "") + '.png';
-		}
-		var text = Zotero.getString(`fileInterface.itemsWereImported`, numItems, numItems);
-		progress.setIcon(icon);
-		progress.setText(text);
-		// For synchronous translators, which don't update progress
-		progress.setProgress(100);
-		progressWin.startCloseTimer(5000);
+		
+		Zotero.debug(`Imported ${numItems} item(s) in ${performance.now() - t} ms`);
+		
+		return true;
 	});
 	
+	
+	var _getMendeleyTranslation = async function () {
+		if (true) {
+			Components.utils.import("chrome://zotero/content/import/mendeley/mendeleyImport.js");
+		}
+		// TEMP: Load uncached from ~/zotero-client for development
+		else {
+			Components.utils.import("resource://gre/modules/FileUtils.jsm");
+			let file = FileUtils.getDir("Home", []);
+			file = OS.Path.join(
+				file.path,
+				'zotero-client', 'chrome', 'content', 'zotero', 'import', 'mendeley', 'mendeleyImport.js'
+			);
+			let fileURI = OS.Path.toFileURI(file);
+			let xmlhttp = await Zotero.HTTP.request(
+				'GET',
+				fileURI,
+				{
+					dontCache: true,
+					responseType: 'text'
+				}
+			);
+			eval(xmlhttp.response);
+		}
+		return new Zotero_Import_Mendeley();
+	}
+	
+	
 	/**
 	 * Creates a bibliography from a collection or saved search
 	 */

chrome/content/zotero/import/importWizard.js

@@ -0,0 +1,332 @@
+var Zotero_Import_Wizard = {
+	_wizard: null,
+	_dbs: null,
+	_file: null,
+	_translation: null,
+	
+	
+	init: async function () {
+		this._wizard = document.getElementById('import-wizard');
+		
+		var dbs = await Zotero_File_Interface.findMendeleyDatabases();
+		if (dbs.length) {
+			document.getElementById('radio-import-source-mendeley').hidden = false;
+		}
+		
+		// If no existing collections or non-trash items in the library, don't create a new
+		// collection by default
+		var args = window.arguments[0].wrappedJSObject;
+		if (args && args.libraryID) {
+			let sql = "SELECT ROWID FROM collections WHERE libraryID=?1 "
+				+ "UNION "
+				+ "SELECT ROWID FROM items WHERE libraryID=?1 "
+				// Not in trash
+				+ "AND itemID NOT IN (SELECT itemID FROM deletedItems) "
+				// And not a child item (which doesn't necessarily show up in the trash)
+				+ "AND itemID NOT IN (SELECT itemID FROM itemNotes WHERE parentItemID IS NOT NULL) "
+				+ "AND itemID NOT IN (SELECT itemID FROM itemAttachments WHERE parentItemID IS NOT NULL) "
+				+ "LIMIT 1";
+			if (!await Zotero.DB.valueQueryAsync(sql, args.libraryID)) {
+				document.getElementById('create-collection-checkbox').removeAttribute('checked');
+			}
+		}
+		
+		Zotero.Translators.init(); // async
+	},
+	
+	
+	onModeChosen: async function () {
+		var wizard = this._wizard;
+		
+		var mode = document.getElementById('import-source').selectedItem.id;
+		try {
+			switch (mode) {
+			case 'radio-import-source-file':
+				await this.chooseFile();
+				break;
+				
+			case 'radio-import-source-mendeley':
+				this._dbs = await Zotero_File_Interface.findMendeleyDatabases();
+				// This shouldn't happen, because we only show the wizard if there are databases
+				if (!this._dbs.length) {
+					throw new Error("No databases found");
+				}
+				this._populateFileList(this._dbs);
+				document.getElementById('file-options-header').textContent
+					= Zotero.getString('fileInterface.chooseAppDatabaseToImport', 'Mendeley')
+				wizard.goTo('page-file-list');
+				wizard.canRewind = true;
+				this._enableCancel();
+				break;
+			
+			default:
+				throw new Error(`Unknown mode ${mode}`);
+			}
+		}
+		catch (e) {
+			this._onDone(
+				Zotero.getString('general.error'),
+				Zotero.getString('fileInterface.importError'),
+				true
+			);
+			throw e;
+		}
+	},
+	
+	
+	goToStart: function () {
+		this._wizard.goTo('page-start');
+		this._wizard.canAdvance = true;
+		return false;
+	},
+	
+	
+	chooseFile: async function (translation) {
+		var translation = new Zotero.Translate.Import();
+		var translators = await translation.getTranslators();
+		const nsIFilePicker = Components.interfaces.nsIFilePicker;
+		var fp = Components.classes["@mozilla.org/filepicker;1"]
+				.createInstance(nsIFilePicker);
+		fp.init(window, Zotero.getString("fileInterface.import"), nsIFilePicker.modeOpen);
+		
+		fp.appendFilters(nsIFilePicker.filterAll);
+		
+		var collation = Zotero.getLocaleCollation();
+		
+		// Add Mendeley DB, which isn't a translator
+		var mendeleyFilter = {
+			label: "Mendeley Database", // TODO: Localize
+			target: "*.sqlite"
+		};
+		var filters = [...translators];
+		filters.push(mendeleyFilter);
+		
+		filters.sort((a, b) => collation.compareString(1, a.label, b.label));
+		for (let filter of filters) {
+			fp.appendFilter(filter.label, "*." + filter.target);
+		}
+		
+		var rv = fp.show();
+		if (rv !== nsIFilePicker.returnOK && rv !== nsIFilePicker.returnReplace) {
+			return false;
+		}
+		
+		Zotero.debug(`File is ${fp.file.path}`);
+		
+		this._file = fp.file.path;
+		this._wizard.canAdvance = true;
+		this._wizard.goTo('page-options');
+	},
+	
+	
+	/**
+	 * When a file is clicked on in the file list
+	 */
+	onFileSelected: async function () {
+		var index = document.getElementById('file-list').selectedIndex;
+		if (index != -1) {
+			this._file = this._dbs[index].path;
+			this._wizard.canAdvance = true;
+		}
+		else {
+			this._file = null;
+			this._wizard.canAdvance = false;
+		}
+	},
+	
+	
+	/**
+	 * When the user clicks "Other…" to choose a file not in the list
+	 */
+	chooseMendeleyDB: async function () {
+		document.getElementById('file-list').selectedIndex = -1;
+		const nsIFilePicker = Components.interfaces.nsIFilePicker;
+		var fp = Components.classes["@mozilla.org/filepicker;1"]
+			.createInstance(nsIFilePicker);
+		fp.init(window, Zotero.getString('fileInterface.import'), nsIFilePicker.modeOpen);
+		fp.appendFilter("Mendeley Database", "*.sqlite"); // TODO: Localize
+		var rv = fp.show();
+		if (rv != nsIFilePicker.returnOK) {
+			return false;
+		}
+		this._file = fp.file.path;
+		this._wizard.canAdvance = true;
+		this._wizard.advance();
+	},
+	
+	
+	onOptionsShown: function () {
+		
+	},
+	
+	
+	onImportStart: async function () {
+		if (!this._file) {
+			let index = document.getElementById('file-list').selectedIndex;
+			this._file = this._dbs[index].path;
+		}
+		this._disableCancel();
+		this._wizard.canRewind = false;
+		this._wizard.canAdvance = false;
+		await this.doImport({
+			createNewCollection: document.getElementById('create-collection-checkbox').hasAttribute('checked')
+		});
+	},
+	
+	
+	onBeforeImport: async function (translation) {
+		// Unrecognized translator
+		if (!translation) {
+			// Allow error dialog to be displayed, and then close window
+			setTimeout(function () {
+				window.close();
+			});
+			return;
+		}
+		
+		this._translation = translation;
+		
+		// Switch to progress pane
+		this._wizard.goTo('page-progress');
+		var pm = document.getElementById('import-progressmeter');
+		
+		translation.setHandler('itemDone', function () {
+			pm.value = translation.getProgress();
+		});
+	},
+	
+	
+	doImport: async function (options) {
+		try {
+			let result = await Zotero_File_Interface.importFile({
+				file: this._file,
+				onBeforeImport: this.onBeforeImport.bind(this),
+				addToLibraryRoot: !options.createNewCollection
+			});
+			
+			// Cancelled by user or due to error
+			if (!result) {
+				window.close();
+				return;
+			}
+			
+			let numItems = this._translation.newItems.length;
+			this._onDone(
+				Zotero.getString('fileInterface.importComplete'),
+				Zotero.getString(`fileInterface.itemsWereImported`, numItems, numItems)
+			);
+		}
+		catch (e) {
+			if (e.message == 'Encrypted Mendeley database') {
+				let url = 'https://www.zotero.org/support/kb/mendeley_import';
+				this._onDone(
+					Zotero.getString('general.error'),
+					// TODO: Localize
+					`The selected Mendeley database cannot be read, likely because it is encrypted. `
+						+ `See <a href="${url}" class="text-link">How do I import a Mendeley library `
+						+ `into Zotero?</a> for more information.`
+				);
+			}
+			else {
+				this._onDone(
+					Zotero.getString('general.error'),
+					Zotero.getString('fileInterface.importError'),
+					true
+				);
+			}
+			throw e;
+		}
+	},
+	
+	
+	reportError: function () {
+		Zotero.getActiveZoteroPane().reportErrors();
+		window.close();
+	},
+	
+	
+	_populateFileList: async function (files) {
+		var listbox = document.getElementById('file-list');
+		
+		// Remove existing entries
+		var items = listbox.getElementsByTagName('listitem');
+		for (let item of items) {
+			listbox.removeChild(item);
+		}
+		
+		for (let file of files) {
+			let li = document.createElement('listitem');
+			
+			let name = document.createElement('listcell');
+			// Simply filenames
+			let nameStr = file.name
+				.replace(/\.sqlite$/, '')
+				.replace(/@www\.mendeley\.com$/, '');
+			if (nameStr == 'online') {
+				nameStr = Zotero.getString('dataDir.default', 'online.sqlite');
+			}
+			name.setAttribute('label', nameStr + ' ');
+			li.appendChild(name);
+			
+			let lastModified = document.createElement('listcell');
+			lastModified.setAttribute('label', file.lastModified.toLocaleString() + ' ');
+			li.appendChild(lastModified);
+			
+			let size = document.createElement('listcell');
+			size.setAttribute(
+				'label',
+				Zotero.getString('general.nMegabytes', (file.size / 1024 / 1024).toFixed(1)) + ' '
+			);
+			li.appendChild(size);
+			
+			listbox.appendChild(li);
+		}
+		
+		if (files.length == 1) {
+			listbox.selectedIndex = 0;
+		}
+	},
+	
+	
+	_enableCancel: function () {
+		this._wizard.getButton('cancel').disabled = false;
+	},
+	
+	
+	_disableCancel: function () {
+		this._wizard.getButton('cancel').disabled = true;
+	},
+	
+	
+	_onDone: function (label, description, showReportErrorButton) {
+		var wizard = this._wizard;
+		wizard.getPageById('page-done').setAttribute('label', label);
+		
+		var xulElem = document.getElementById('result-description');
+		var htmlElem = document.getElementById('result-description-html');
+		
+		if (description.includes('href')) {
+			htmlElem.innerHTML = description;
+			Zotero.Utilities.Internal.updateHTMLInXUL(htmlElem);
+			xulElem.hidden = true;
+			htmlElem.setAttribute('display', 'block');
+		}
+		else {
+			xulElem.textContent = description;
+			xulElem.hidden = false;
+			htmlElem.setAttribute('display', 'none');
+		}
+		document.getElementById('result-description')
+		
+		if (showReportErrorButton) {
+			let button = document.getElementById('result-report-error');
+			button.setAttribute('label', Zotero.getString('errorReport.reportError'));
+			button.hidden = false;
+		}
+		
+		// When done, move to last page and allow closing
+		wizard.canAdvance = true;
+		wizard.goTo('page-done');
+		wizard.canRewind = false;
+	}
+};

chrome/content/zotero/import/importWizard.xul

@@ -0,0 +1,75 @@
+<?xml version="1.0"?>
+
+<?xml-stylesheet href="chrome://global/skin/" type="text/css"?>
+<?xml-stylesheet href="chrome://zotero/skin/importWizard.css" type="text/css"?>
+
+<!DOCTYPE window SYSTEM "chrome://zotero/locale/zotero.dtd">
+
+<wizard id="import-wizard"
+		xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"
+		xmlns:html="http://www.w3.org/1999/xhtml"
+		title="&zotero.import;"
+		onload="Zotero_Import_Wizard.init()">
+	
+	<script src="../include.js"/>
+	<script src="../fileInterface.js"/>
+	<script src="importWizard.js"/>
+	
+	<wizardpage pageid="page-start"
+			label="&zotero.import.whereToImportFrom;"
+			next="page-options"
+			onpageadvanced="Zotero_Import_Wizard.onModeChosen(); return false;">
+		<radiogroup id="import-source">
+			<radio id="radio-import-source-file" label="&zotero.import.source.file;"/>
+			<radio id="radio-import-source-mendeley" label="Mendeley" hidden="true"/>
+		</radiogroup>
+	</wizardpage>
+	
+	<wizardpage pageid="page-file-list"
+			next="page-options"
+			onpagerewound="return Zotero_Import_Wizard.goToStart()">
+		<description id="file-options-header"/>
+		<listbox id="file-list" onselect="Zotero_Import_Wizard.onFileSelected()">
+			<listhead>
+				<listheader label="&zotero.import.database;"/>
+				<listheader label="&zotero.import.lastModified;"/>
+				<listheader label="&zotero.import.size;"/>
+			</listhead>
+			
+			<listcols>
+				<listcol flex="1"/>
+				<listcol/>
+				<listcol/>
+			</listcols>
+		</listbox>
+		<hbox>
+			<button label="&zotero.general.other;" oncommand="Zotero_Import_Wizard.chooseMendeleyDB()"/>
+		</hbox>
+	</wizardpage>
+	
+	<wizardpage pageid="page-options"
+			label="&zotero.general.options;"
+			next="page-progress"
+			onpageshow="Zotero_Import_Wizard.onOptionsShown()"
+			onpagerewound="return Zotero_Import_Wizard.goToStart()"
+			onpageadvanced="Zotero_Import_Wizard.onImportStart()">
+		<checkbox id="create-collection-checkbox" label="&zotero.import.createCollection;" checked="true" />
+	</wizardpage>
+	
+	<wizardpage pageid="page-progress"
+			label="&zotero.import.importing;"
+			onpageshow="document.getElementById('import-wizard').canRewind = false;"
+			next="page-done">
+		<progressmeter id="import-progressmeter" mode="determined"/>
+	</wizardpage>
+	
+	<wizardpage pageid="page-done">
+		<description id="result-description"/>
+		<html:div id="result-description-html"/>
+		<hbox>
+			<button id="result-report-error"
+				oncommand="Zotero_Import_Wizard.reportError()"
+				hidden="true"/>
+		</hbox>
+	</wizardpage>
+</wizard>

chrome/content/zotero/import/mendeley/mendeleySchemaMap.js

@@ -0,0 +1,102 @@
+var map = {
+	83: {
+		itemTypes: {
+			Bill: "bill",
+			Book: "book",
+			BookSection: "bookSection",
+			Case: "case",
+			ComputerProgram: "computerProgram",
+			ConferenceProceedings: "conferencePaper",
+			EncyclopediaArticle: "encyclopediaArticle",
+			Film: "film",
+			Generic: "document",
+			JournalArticle: "journalArticle",
+			MagazineArticle: "magazineArticle",
+			NewspaperArticle: "newspaperArticle",
+			Patent: "patent",
+			Report: "report",
+			Statute: "statute",
+			TelevisionBroadcast: "tvBroadcast",
+			Thesis: "thesis",
+			WebPage: "webpage",
+			WorkingPaper: "report"
+		},
+		fields: {
+			id: "",
+			uuid: "",
+			reviewedArticle: "",
+			revisionNumber: "",
+			publisher: "publisher",
+			reprintEdition: "",
+			series: "seriesTitle",
+			seriesNumber: "seriesNumber",
+			sections: "section",
+			seriesEditor: "creator[seriesEditor]", // falls back to editor if necessary
+			owner: "",
+			pages: "func[pages]",
+			month: "", // handled explicitly
+			originalPublication: "",
+			publication: "publicationTitle",
+			publicLawNumber: "publicLawNumber",
+			pmid: "extra[PMID]",
+			sourceType: "",
+			session: "session",
+			shortTitle: "shortTitle",
+			volume: "volume",
+			year: "", // handled explicitly
+			userType: "type",
+			country: "place[country]",
+			dateAccessed: "accessDate",
+			committee: "committee",
+			counsel: "creator[counsel]",
+			doi: "DOI",
+			edition: "edition",
+			day: "", // handled explicitly
+			department: "",
+			citationKey: "citationKey", // put in Extra
+			city: "place[city]",
+			chapter: "",
+			codeSection: "section",
+			codeVolume: "codeVolume",
+			code: "code",
+			codeNumber: "codeNumber",
+			issue: "issue",
+			language: "language",
+			isbn: "ISBN",
+			issn: "ISSN",
+			length: "",
+			medium: "medium",
+			lastUpdate: "",
+			legalStatus: "legalStatus",
+			hideFromMendeleyWebIndex: "",
+			institution: "publisher",
+			genre: "genre",
+			internationalTitle: "",
+			internationalUserType: "",
+			internationalAuthor: "",
+			internationalNumber: "",
+			deletionPending: "",
+			favourite: "", // tag?
+			confirmed: "", // tag?
+			deduplicated: "",
+			read: "", // tag?
+			type: "", // item type handled separately
+			title: "title",
+			privacy: "",
+			applicationNumber: "applicationNumber",
+			arxivId: "extra[arXiv]",
+			advisor: "",
+			articleColumn: "",
+			modified: "func[fromUnixtime:dateModified]",
+			abstract: "abstractNote",
+			added: "func[fromUnixtime:dateAdded]",
+			note: "func[note]",
+			importer: ""
+		},
+		creatorTypes: {
+			DocumentAuthor: "author",
+			DocumentEditor: "editor",
+			DocumentTranslator: "translator"
+		}
+	}
+};

chrome/content/zotero/integration/addCitationDialog.js

@@ -59,10 +59,8 @@ var Zotero_Citation_Dialog = new function () {
 	this.listItemSelected = listItemSelected;
 	this.up = up;
 	this.down = down;
-	this.add = add;
 	this.remove = remove;
 	this.setSortToggle = setSortToggle;
-	this.citationSortUnsort = citationSortUnsort;
 	this.confirmRegenerate = confirmRegenerate;
 	this.accept = accept;
 	this.cancel = cancel;
@@ -373,13 +371,13 @@ var Zotero_Citation_Dialog = new function () {
 	/*
 	 * Adds an item to the multipleSources list
 	 */
-	function add(first_item) {
+	this.add = Zotero.Promise.coroutine(function* (first_item) {
 		
 		var pos, len;
 		var item = itemsView.getSelectedItems()[0]; // treeview from xpcom/itemTreeView.js
 		
 		if (!item) {
-			sortCitation();
+			yield sortCitation();
 			_updateAccept();
 			_updatePreview();
 			return;
@@ -412,11 +410,11 @@ var Zotero_Citation_Dialog = new function () {
 		_citationList.ensureElementIsVisible(selectionNode);
 
 		// allow user to press OK
-		selectionNode = sortCitation(selectionNode);
+		selectionNode = yield sortCitation(selectionNode);
 		_citationList.selectItem(selectionNode);
 		_updateAccept();
 		_updatePreview();
-	}
+	});
 	
 	/*
 	 * Deletes a citation from the multipleSources list
@@ -446,11 +444,11 @@ var Zotero_Citation_Dialog = new function () {
 	/*
 	 * Sorts preview citations, if preview is open.
 	 */
-	function citationSortUnsort() {
+	this.citationSortUnsort = Zotero.Promise.coroutine(function* () {
 		setSortToggle();
-		sortCitation();
+		yield sortCitation();
 		_updatePreview();
-	}
+	});
 
 	/*
 	 * Sets the current sort toggle state persistently on the citation.
@@ -468,7 +466,7 @@ var Zotero_Citation_Dialog = new function () {
 	/*
 	 * Sorts the list of citations
  	 */
-	function sortCitation(scrollToItem) {
+	var sortCitation = Zotero.Promise.coroutine(function* (scrollToItem) {
  		if(!_sortCheckbox) return scrollToItem;
  		if(!_sortCheckbox.checked) {
  			io.citation.properties.unsorted = true;
@@ -485,7 +483,7 @@ var Zotero_Citation_Dialog = new function () {
 		
 		// run preview function to re-sort, if it hasn't already been
 		// run
-		io.sort();
+		yield io.sort();
 		
 		// add items back to list
 		scrollToItem = null;
@@ -502,7 +500,7 @@ var Zotero_Citation_Dialog = new function () {
 		
 		if(scrollToItem) _citationList.ensureElementIsVisible(scrollToItem);
 		return scrollToItem;
-	}
+	});
 	
 	/*
 	 * Ask whether to modifiy the preview

chrome/content/zotero/integration/editBibliographyDialog.js

@@ -74,8 +74,8 @@ var Zotero_Bibliography_Dialog = new function () {
 		if(selectedItemIDs.length) {
 			for (let itemID of selectedItemIDs) {
 				var itemIndexToSelect = false;
-				for(var i in bibEditInterface.bibliography[0].entry_ids) {
-					if(bibEditInterface.bibliography[0].entry_ids[i].indexOf(itemID) !== -1) {
+				for(var i in bibEditInterface.bib[0].entry_ids) {
+					if(bibEditInterface.bib[0].entry_ids[i].indexOf(itemID) !== -1) {
 						itemIndexToSelect = i;
 						continue;
 					}
@@ -254,7 +254,7 @@ var Zotero_Bibliography_Dialog = new function () {
 	 */
 	function _getSelectedListItemIDs() {
 		return Array.from(_itemList.selectedItems)
-			.map(item => bibEditInterface.bibliography[0].entry_ids[item.value][0]);
+			.map(item => bibEditInterface.bib[0].entry_ids[item.value][0]);
 	}
 	
 	/**
@@ -287,8 +287,8 @@ var Zotero_Bibliography_Dialog = new function () {
 		
 		editor.readonly = index === undefined;
 		if(index !== undefined) {
-			var itemID = bibEditInterface.bibliography[0].entry_ids[index];
-			editor.value = bibEditInterface.bibliography[1][index];
+			var itemID = bibEditInterface.bib[0].entry_ids[index];
+			editor.value = bibEditInterface.bib[1][index];
 			_lastSelectedIndex = index;
 			_lastSelectedItemID = itemID;
 			_lastSelectedValue = editor.value;
@@ -304,7 +304,7 @@ var Zotero_Bibliography_Dialog = new function () {
 	 * loads items from itemSet
 	 */
 	function _loadItems() {
-		var itemIDs = bibEditInterface.bibliography[0].entry_ids;
+		var itemIDs = bibEditInterface.bib[0].entry_ids;
 		var items = itemIDs.map(itemID => Zotero.Cite.getItem(itemID[0]));
 		
 		// delete all existing items from list

chrome/content/zotero/integration/integrationDocPrefs.xul

@@ -31,10 +31,11 @@
 <dialog
 	id="zotero-doc-prefs-dialog"
 	orient="vertical"
-	buttons="accept,cancel"
+	buttons="accept,cancel,help"
 	title="&zotero.integration.docPrefs.title;"
 	onload="Zotero_File_Interface_Bibliography.init();"
 	ondialogaccept="Zotero_File_Interface_Bibliography.acceptSelection();"
+	ondialoghelp="Zotero_File_Interface_Bibliography.openHelpLink();"
 	onclose="document.documentElement.cancelDialog(); event.preventDefault(); event.stopPropagation();"
 	xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"
 	persist="screenX screenY"
@@ -52,7 +53,7 @@
 			</hbox>
 		</groupbox>
 		
-		<groupbox>
+		<groupbox id="locale-box">
 			<hbox align="center">
 				<caption label="&zotero.bibliography.locale.label;"/>
 				<menulist id="locale-menu" oncommand="Zotero_File_Interface_Bibliography.localeChanged(this.selectedItem.value)"/>
@@ -67,7 +68,7 @@
 			</radiogroup>
 		</groupbox>
 		
-		<groupbox>
+		<groupbox id="formatUsing-groupbox">
 			<caption label="&zotero.integration.prefs.formatUsing.label;"/>
 			
 			<radiogroup id="formatUsing" orient="vertical">
@@ -84,5 +85,10 @@
 			<checkbox id="automaticJournalAbbreviations-checkbox" label="&zotero.integration.prefs.automaticJournalAbbeviations.label;"/>
 			<description class="radioDescription">&zotero.integration.prefs.automaticJournalAbbeviations.caption;</description>
 		</vbox>
+		
+		<vbox id="automaticCitationUpdates-vbox">
+			<checkbox id="automaticCitationUpdates-checkbox" label="&zotero.integration.prefs.automaticCitationUpdates.label;" tooltiptext="&zotero.integration.prefs.automaticCitationUpdates.tooltip;"/>
+			<description class="radioDescription">&zotero.integration.prefs.automaticCitationUpdates.description;</description>
+		</vbox>
 	</vbox>
 </dialog>

chrome/content/zotero/integration/progressBar.js

@@ -0,0 +1,121 @@
+/*
+    ***** BEGIN LICENSE BLOCK *****
+    
+    Copyright © 2018 Center for History and New Media
+				     George Mason University, Fairfax, Virginia, USA
+				     http://zotero.org
+    
+    This file is part of Zotero.
+    
+    Zotero is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Zotero is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+    
+    You should have received a copy of the GNU Affero General Public License
+    along with Zotero.  If not, see <http://www.gnu.org/licenses/>.
+    
+    ***** END LICENSE BLOCK *****
+*/
+Components.utils.import("resource://gre/modules/Services.jsm");
+
+var Zotero_ProgressBar = new function () {
+	var initialized, io;
+	
+	/**
+	 * Pre-initialization, when the dialog has loaded but has not yet appeared
+	 */
+	this.onDOMContentLoaded = function(event) {
+		if(event.target === document) {
+			initialized = true;
+			io = window.arguments[0].wrappedJSObject;
+			if (io.onLoad) {
+				io.onLoad(_onProgress);
+			}
+			
+			// Only hide chrome on Windows or Mac
+			if(Zotero.isMac) {
+				document.documentElement.setAttribute("drawintitlebar", true);
+			} else if(Zotero.isWin) {
+				document.documentElement.setAttribute("hidechrome", true);
+			}
+			
+			new WindowDraggingElement(document.getElementById("quick-format-dialog"), window);
+		
+		}
+	};
+	
+	/**
+	 * Center the window
+	 */
+	this.onLoad = function(event) {
+		if(event.target !== document) return;		
+		// make sure we are visible
+		window.focus();
+		window.setTimeout(function() {
+			var targetX = Math.floor(-window.outerWidth/2 + (window.screen.width / 2));
+			var targetY = Math.floor(-window.outerHeight/2 + (window.screen.height / 2));
+			Zotero.debug("Moving window to "+targetX+", "+targetY);
+			window.moveTo(targetX, targetY);
+		}, 0);
+	};
+	
+	/**
+	 * Called when progress changes
+	 */
+	function _onProgress(percent) {
+		var meter = document.getElementById("quick-format-progress-meter");
+		if(percent === null) {
+			meter.mode = "undetermined";
+		} else {
+			meter.mode = "determined";
+			meter.value = Math.round(percent);
+		}
+	}
+	
+	/**
+	 * Resizes windows
+	 * @constructor
+	 */
+	var Resizer = function(panel, targetWidth, targetHeight, pixelsPerStep, stepsPerSecond) {
+		this.panel = panel;
+		this.curWidth = panel.clientWidth;
+		this.curHeight = panel.clientHeight;
+		this.difX = (targetWidth ? targetWidth - this.curWidth : 0);
+		this.difY = (targetHeight ? targetHeight - this.curHeight : 0);
+		this.step = 0;
+		this.steps = Math.ceil(Math.max(Math.abs(this.difX), Math.abs(this.difY))/pixelsPerStep);
+		this.timeout = (1000/stepsPerSecond);
+		
+		var me = this;
+		this._animateCallback = function() { me.animate() };
+	};
+	
+	/**
+	 * Performs a step of the animation
+	 */
+	Resizer.prototype.animate = function() {
+		if(this.stopped) return;
+		this.step++;
+		this.panel.sizeTo(this.curWidth+Math.round(this.step*this.difX/this.steps),
+			this.curHeight+Math.round(this.step*this.difY/this.steps));
+		if(this.step !== this.steps) {
+			window.setTimeout(this._animateCallback, this.timeout);
+		}
+	};
+	
+	/**
+	 * Halts resizing
+	 */
+	Resizer.prototype.stop = function() {
+		this.stopped = true;
+	};
+}
+
+window.addEventListener("DOMContentLoaded", Zotero_ProgressBar.onDOMContentLoaded, false);
+window.addEventListener("load", Zotero_ProgressBar.onLoad, false);

chrome/content/zotero/integration/progressBar.xul

@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<!--
+    ***** BEGIN LICENSE BLOCK *****
+    
+    Copyright © 2018 Center for History and New Media
+                     George Mason University, Fairfax, Virginia, USA
+                     http://zotero.org
+    
+    This file is part of Zotero.
+    
+    Zotero is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Zotero is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+    
+    You should have received a copy of the GNU Affero General Public License
+    along with Zotero.  If not, see <http://www.gnu.org/licenses/>.
+    
+    ***** END LICENSE BLOCK *****
+-->
+<?xml-stylesheet href="chrome://global/skin/" type="text/css"?>
+<?xml-stylesheet href="chrome://global/skin/browser.css" type="text/css"?>
+<?xml-stylesheet href="chrome://zotero/skin/zotero.css" type="text/css"?>
+<?xml-stylesheet href="chrome://zotero/skin/integration.css" type="text/css"?>
+<?xml-stylesheet href="chrome://zotero-platform/content/integration.css" type="text/css"?>
+<!DOCTYPE window SYSTEM "chrome://zotero/locale/zotero.dtd">
+
+<window
+	id="quick-format-dialog"
+	class="progress-bar"
+	orient="vertical"
+	title="&zotero.progress.title;"
+	xmlns:html="http://www.w3.org/1999/xhtml"
+	xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"
+	persist="screenX screenY">
+	
+	<script src="../include.js"/>
+	<script src="windowDraggingUtils.js" type="text/javascript"/>
+	<script src="progressBar.js" type="text/javascript"/>
+	
+	<box orient="horizontal" id="quick-format-entry"> 
+		<deck id="quick-format-deck" selectedIndex="0" flex="1">
+			<progressmeter id="quick-format-progress-meter" mode="undetermined" value="0" flex="1"/>
+		</deck>
+	</box>
+</window>

chrome/content/zotero/integration/quickFormat.js

@@ -37,9 +37,10 @@ var Zotero_QuickFormat = new function () {
 		keepSorted,  showEditor, referencePanel, referenceBox, referenceHeight = 0,
 		separatorHeight = 0, currentLocator, currentLocatorLabel, currentSearchTime, dragging,
 		panel, panelPrefix, panelSuffix, panelSuppressAuthor, panelLocatorLabel, panelLocator,
-		panelLibraryLink, panelInfo, panelRefersToBubble, panelFrameHeight = 0, accepted = false,
-		searchTimeout;
+		panelLibraryLink, panelInfo, panelRefersToBubble, panelFrameHeight = 0, accepted = false;
+	var _searchPromise;
 	
+	const SEARCH_TIMEOUT = 250;
 	const SHOWN_REFERENCES = 7;
 	
 	/**
@@ -178,6 +179,7 @@ var Zotero_QuickFormat = new function () {
 	 */
 	function _getCurrentEditorTextNode() {
 		var selection = qfiWindow.getSelection();
+		if (!selection) return false;
 		var range = selection.getRangeAt(0);
 		
 		var node = range.startContainer;
@@ -710,7 +712,7 @@ var Zotero_QuickFormat = new function () {
 	/**
 	 * Converts the selected item to a bubble
 	 */
-	function _bubbleizeSelected() {
+	var _bubbleizeSelected = Zotero.Promise.coroutine(function* () {
 		if(!referenceBox.hasChildNodes() || !referenceBox.selectedItem) return false;
 		
 		var citationItem = {"id":referenceBox.selectedItem.getAttribute("zotero-item")};
@@ -733,11 +735,11 @@ var Zotero_QuickFormat = new function () {
 		node.nodeValue = "";
 		var bubble = _insertBubble(citationItem, node);
 		_clearEntryList();
-		_previewAndSort();
+		yield _previewAndSort();
 		_refocusQfe();
 		
 		return true;
-	}
+	});
 	
 	/**
 	 * Ignores clicks (for use on separators in the rich list box)
@@ -901,13 +903,13 @@ var Zotero_QuickFormat = new function () {
 	/**
 	 * Generates the preview and sorts citations
 	 */
-	function _previewAndSort() {
+	var _previewAndSort = Zotero.Promise.coroutine(function* () {
 		var shouldKeepSorted = keepSorted.hasAttribute("checked"),
 			editorShowing = showEditor.hasAttribute("checked");
 		if(!shouldKeepSorted && !editorShowing) return;
 		
 		_updateCitationObject();
-		io.sort();
+		yield io.sort();
 		if(shouldKeepSorted) {
 			// means we need to resort citations
 			_clearCitation();
@@ -919,7 +921,7 @@ var Zotero_QuickFormat = new function () {
 			
 			_moveCursorToEnd();
 		}
-	}
+	});
 	
 	/**
 	 * Shows the citation properties panel for a given bubble
@@ -1051,14 +1053,26 @@ var Zotero_QuickFormat = new function () {
 	 * keypress, since searches can be slow.
 	 */
 	function _resetSearchTimer() {
-		if(searchTimeout) clearTimeout(searchTimeout);
-		searchTimeout = setTimeout(_quickFormat, 250);
+		// Show spinner
+		var spinner = document.getElementById('quick-format-spinner');
+		spinner.style.visibility = '';
+		// Cancel current search if active
+		if (_searchPromise && _searchPromise.isPending()) {
+			_searchPromise.cancel();
+		}
+		// Start new search
+		_searchPromise = Zotero.Promise.delay(SEARCH_TIMEOUT)
+			.then(() => _quickFormat())
+			.then(() => {
+				_searchPromise = null;
+				spinner.style.visibility = 'hidden';
+			});
 	}
 	
 	/**
 	 * Handle return or escape
 	 */
-	function _onQuickSearchKeyPress(event) {
+	var _onQuickSearchKeyPress = Zotero.Promise.coroutine(function* (event) {
 		// Prevent hang if another key is pressed after Enter
 		// https://forums.zotero.org/discussion/59157/
 		if (accepted) {
@@ -1070,7 +1084,7 @@ var Zotero_QuickFormat = new function () {
 		var keyCode = event.keyCode;
 		if (keyCode === event.DOM_VK_RETURN) {
 			event.preventDefault();
-			if(!_bubbleizeSelected() && !_getEditorContent()) {
+			if(!(yield _bubbleizeSelected()) && !_getEditorContent()) {
 				_accept();
 			}
 		} else if(keyCode === event.DOM_VK_TAB || event.charCode === 59 /* ; */) {
@@ -1149,7 +1163,7 @@ var Zotero_QuickFormat = new function () {
 		} else {
 			_resetSearchTimer();
 		}
-	}
+	});
 	
 	/**
 	 * Adds a dummy element to make dragging work
@@ -1177,7 +1191,7 @@ var Zotero_QuickFormat = new function () {
 	/**
 	 * Replaces the dummy element with a node to make dropping work
 	 */
-	function _onBubbleDrop(event) {
+	var _onBubbleDrop = Zotero.Promise.coroutine(function* (event) {
 		event.preventDefault();
 		event.stopPropagation();
 
@@ -1195,9 +1209,9 @@ var Zotero_QuickFormat = new function () {
 			keepSorted.removeAttribute("checked");
 		}
 
-		_previewAndSort();
+		yield _previewAndSort();
 		_moveCursorToEnd();
-	}
+	});
 	
 	/**
 	 * Handle a click on a bubble
@@ -1320,7 +1334,7 @@ var Zotero_QuickFormat = new function () {
 		pane.selectItem(id);
 		
 		// Pull window to foreground
-		Zotero.Integration.activate(pane.document.defaultView);
+		Zotero.Utilities.Internal.activate(pane.document.defaultView);
 	}
 	
 	/**

chrome/content/zotero/integration/quickFormat.xul

@@ -62,6 +62,9 @@
 					</toolbarbutton>
 					<iframe id="quick-format-iframe" ondragstart="event.stopPropagation()" src="data:application/xhtml+xml,%3C!DOCTYPE%20html%20PUBLIC%20%22-//W3C//DTD%20XHTML%201.0%20Strict//EN%22%20%22http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd%22%3E%3Chtml%20xmlns=%22http://www.w3.org/1999/xhtml%22%3E%3Chead%3E%3Clink%20rel=%22stylesheet%22%20type=%22text/css%22%20href=%22chrome://zotero/skin/integration.css%22/%3E%3Clink%20rel=%22stylesheet%22%20type=%22text/css%22%20href=%22chrome://zotero-platform/content/integration.css%22/%3E%3C/head%3E%3Cbody%20contenteditable=%22true%22%20spellcheck=%22false%22%20id=%22quick-format-editor%22/%3E%3C/html%3E"
 						tabindex="1" flex="1"/>
+					<vbox id="quick-format-spinner" style="visibility: hidden">
+						<image class="zotero-spinner-16"/>
+					</vbox>
 				</hbox>
 			</hbox>
 			<progressmeter id="quick-format-progress-meter" mode="undetermined" value="0" flex="1"/>

chrome/content/zotero/itemPane.js

@@ -25,6 +25,7 @@
 
 var ZoteroItemPane = new function() {
 	var _lastItem, _itemBox, _notesLabel, _notesButton, _notesList, _tagsBox, _relatedBox;
+	var _selectedNoteID;
 	var _translationTarget;
 	var _noteIDs;
 	
@@ -222,6 +223,61 @@ var ZoteroItemPane = new function() {
 	});
 	
 	
+	this.onNoteSelected = function (item, editable) {
+		_selectedNoteID = item.id;
+		
+		// If an external note window is open for this item, don't show the editor
+		if (ZoteroPane.findNoteWindow(item.id)) {
+			this.showNoteWindowMessage();
+			return;
+		}
+		
+		var noteEditor = document.getElementById('zotero-note-editor');
+		
+		// If loading new or different note, disable undo while we repopulate the text field
+		// so Undo doesn't end up clearing the field. This also ensures that Undo doesn't
+		// undo content from another note into the current one.
+		var clearUndo = noteEditor.item ? noteEditor.item.id != item.id : false;
+		
+		noteEditor.mode = editable ? 'edit' : 'view';
+		noteEditor.parent = null;
+		noteEditor.item = item;
+		
+		if (clearUndo) {
+			noteEditor.clearUndo();
+		}
+		
+		document.getElementById('zotero-view-note-button').hidden = !editable;
+		document.getElementById('zotero-item-pane-content').selectedIndex = 2;
+	};
+	
+	
+	this.showNoteWindowMessage = function () {
+		ZoteroPane.setItemPaneMessage(Zotero.getString('pane.item.notes.editingInWindow'));
+	};
+	
+	
+	/**
+	 * Select the parent item and open the note editor
+	 */
+	this.openNoteWindow = async function () {
+		var selectedNote = Zotero.Items.get(_selectedNoteID);
+		
+		// We don't want to show the note in two places, since it causes unnecessary UI updates
+		// and can result in weird bugs where note content gets lost.
+		//
+		// If this is a child note, select the parent
+		if (selectedNote.parentID) {
+			await ZoteroPane.selectItem(selectedNote.parentID);
+		}
+		// Otherwise, hide note and replace with a message that we're editing externally
+		else {
+			this.showNoteWindowMessage();
+		}
+		ZoteroPane.openNoteWindow(selectedNote.id);
+	};
+	
+	
 	this.addNote = function (popup) {
 		ZoteroPane_Local.newNote(popup, _lastItem.key);
 	}
@@ -321,30 +377,18 @@ var ZoteroItemPane = new function() {
 		ZoteroItemPane.setTranslateButton();
 	};
 	
-		
-	this.setToggleReadLabel = function() {
-		var markRead = false;
-		var items = ZoteroPane_Local.itemsView.getSelectedItems();
-		for (let item of items) {
-			if (!item.isRead) {
-				markRead = true;
-				break;
-			}
-		}
+	
+	this.setReadLabel = function (isRead) {
 		var elem = document.getElementById('zotero-feed-item-toggleRead-button');
-		if (markRead) {
-			var label = Zotero.getString('pane.item.markAsRead');
-		} else {
-			label = Zotero.getString('pane.item.markAsUnread');
-		}
+		var label = Zotero.getString('pane.item.' + (isRead ? 'markAsUnread' : 'markAsRead'));
 		elem.setAttribute('label', label);
 
 		var key = Zotero.Keys.getKeyForCommand('toggleRead');
 		var tooltip = label + (Zotero.rtl ? ' \u202B' : ' ') + '(' + key + ')'
 		elem.setAttribute('tooltiptext', tooltip);
 	};
-
-
+	
+	
 	function _updateNoteCount() {
 		var c = _notesList.childNodes.length;
 		

chrome/content/zotero/itemPane.xul

@@ -114,7 +114,9 @@
 				<zoteronoteeditor id="zotero-note-editor" flex="1" notitle="1"
 					previousfocus="zotero-items-tree"
 					onerror="ZoteroPane.displayErrorMessage(); this.mode = 'view'"/>
-				<button id="zotero-view-note-button" label="&zotero.notes.separate;" oncommand="ZoteroPane_Local.openNoteWindow(this.getAttribute('noteID')); if(this.hasAttribute('sourceID')) ZoteroPane_Local.selectItem(this.getAttribute('sourceID'));"/>
+				<button id="zotero-view-note-button"
+						label="&zotero.notes.separate;"
+						oncommand="ZoteroItemPane.openNoteWindow()"/>
 			</groupbox>
 			
 			<!-- Attachment item -->

chrome/content/zotero/locale/csl

@@ -1 +1 @@
-Subproject commit da68506f8f47089d28a8289db75f2f5b7f8e5000
+Subproject commit b8c370c8a978790d2aeefa302f05f3bfb1478e75

chrome/content/zotero/lookup.js

@@ -92,6 +92,45 @@ var Zotero_Lookup = new function () {
 		return false;
 	});
 	
+	
+	this.showPanel = function (button) {
+		var panel = document.getElementById('zotero-lookup-panel');
+		panel.openPopup(button, "after_start", 16, -2, false, false);
+	}
+	
+	
+	/**
+	 * Focuses the field
+	 */
+	this.onShowing = function (event) {
+		// Ignore context menu
+		if (event.originalTarget.id != 'zotero-lookup-panel') return;
+		
+		document.getElementById("zotero-lookup-panel").style.padding = "10px";
+		this.getActivePanel().getElementsByTagName('textbox')[0].focus();
+	}
+	
+	
+	/**
+	 * Cancels the popup and resets fields
+	 */
+	this.onHidden = function (event) {
+		// Ignore context menu
+		if (event.originalTarget.id != 'zotero-lookup-panel') return;
+		
+		document.getElementById("zotero-lookup-textbox").value = "";
+		document.getElementById("zotero-lookup-multiline-textbox").value = "";
+		Zotero_Lookup.toggleProgress(false);
+	}
+	
+	
+	this.getActivePanel = function() {
+		var mlPanel = document.getElementById("zotero-lookup-multiline");
+		if (mlPanel.collapsed) return document.getElementById("zotero-lookup-singleLine");
+		return mlPanel;
+	}
+	
+	
 	/**
 	 * Handles a key press
 	 */
@@ -114,44 +153,27 @@ var Zotero_Lookup = new function () {
 		return true;
 	}
 	
-	/**
-	 * Focuses the field
-	 */
-	this.onShowing = function() {
-		document.getElementById("zotero-lookup-panel").style.padding = "10px";
-		
-		// Workaround for field being truncated in middle
-		// https://github.com/zotero/zotero/issues/343
-		this.toggleMultiline(true);
-		
-		var identifierElement = Zotero_Lookup.toggleMultiline(false);
-		Zotero_Lookup.toggleProgress(false);
-		identifierElement.focus();
-	}
 	
-	/**
-	 * Cancels the popup and resets fields
-	 */
-	this.onHidden = function() {
-		var txtBox = Zotero_Lookup.toggleMultiline(false);
-		var mlTextbox = document.getElementById("zotero-lookup-multiline-textbox");
-		txtBox.value = "";
-		mlTextbox.value = "";
-	}
-
+	this.onInput = function (event, textbox) {
+		this.adjustTextbox(textbox);
+	};
+	
+	
 	/**
 	 * Converts the textbox to multiline if newlines are detected
 	 */
-	this.adjustTextbox = function(txtBox) {
-		if(txtBox.value.trim().match(/[\r\n]/)) {
+	this.adjustTextbox = function (textbox) {
+		if (textbox.value.trim().match(/[\r\n]/)) {
 			Zotero_Lookup.toggleMultiline(true);
-		} else {
-			//since we ignore trailing and leading newlines, we should also trim them for display
-			//can't use trim, because then we cannot add leading/trailing spaces to the single line textbox
-			txtBox.value = txtBox.value.replace(/^([ \t]*[\r\n]+[ \t]*)+|([ \t]*[\r\n]+[ \t]*)+$/g,"");
+		}
+		// Since we ignore trailing and leading newlines, we should also trim them for display
+		// can't use trim, because then we cannot add leading/trailing spaces to the single line textbox
+		else {
+			textbox.value = textbox.value.replace(/^([ \t]*[\r\n]+[ \t]*)+|([ \t]*[\r\n]+[ \t]*)+$/g,"");
 		}
 	}
-
+	
+	
 	/**
 	 * Performs the switch to multiline textbox and returns that textbox
 	 */
@@ -184,21 +206,20 @@ var Zotero_Lookup = new function () {
 	}
 
 	this.toggleProgress = function(on) {
+		// In Firefox 52.6.0, progressmeters burn CPU at idle on Linux when undetermined, even
+		// if they're hidden. (Being hidden is enough on macOS.)
+		var mode = on ? 'undetermined' : 'determined';
+		
 		//single line
 		var txtBox = document.getElementById("zotero-lookup-textbox");
 		txtBox.style.opacity = on ? 0.5 : 1;
 		txtBox.disabled = !!on;
-		document.getElementById("zotero-lookup-progress").setAttribute("collapsed", !on);
+		var p1 = document.getElementById("zotero-lookup-progress");
+		p1.mode = mode;
 
 		//multiline
 		document.getElementById("zotero-lookup-multiline-textbox").disabled = !!on;
-		document.getElementById("zotero-lookup-multiline-progress").setAttribute("collapsed", !on);
-	}
-
-	this.getActivePanel = function() {
-		var mlPanel = document.getElementById("zotero-lookup-multiline");
-		if(mlPanel.collapsed) return document.getElementById("zotero-lookup-singleLine");
-
-		return mlPanel;
+		var p2 = document.getElementById("zotero-lookup-multiline-progress");
+		p2.mode = mode;
 	}
 }

chrome/content/zotero/note.js

@@ -26,10 +26,9 @@
 var noteEditor;
 var notifierUnregisterID;
 
-function onLoad() {
+async function onLoad() {
 	noteEditor = document.getElementById('zotero-note-editor');
 	noteEditor.mode = 'edit';
-	noteEditor.focus();
 	
 	// Set font size from pref
 	Zotero.setFontSize(noteEditor);
@@ -37,42 +36,31 @@ function onLoad() {
 	if (window.arguments) {
 		var io = window.arguments[0];
 	}
+	
 	var itemID = parseInt(io.itemID);
 	var collectionID = parseInt(io.collectionID);
 	var parentItemKey = io.parentItemKey;
 	
-	return Zotero.spawn(function* () {
-		if (itemID) {
-			var ref = yield Zotero.Items.getAsync(itemID);
-			
-			var clearUndo = noteEditor.item ? noteEditor.item.id != ref.id : false;
-			
-			noteEditor.item = ref;
-			
-			// If loading new or different note, disable undo while we repopulate the text field
-			// so Undo doesn't end up clearing the field. This also ensures that Undo doesn't
-			// undo content from another note into the current one.
-			if (clearUndo) {
-				noteEditor.clearUndo();
-			}
-			
-			document.title = ref.getNoteTitle();
+	if (itemID) {
+		var ref = await Zotero.Items.getAsync(itemID);
+		noteEditor.item = ref;
+		document.title = ref.getNoteTitle();
+	}
+	else {
+		if (parentItemKey) {
+			var ref = Zotero.Items.getByLibraryAndKey(parentItemKey);
+			noteEditor.parentItem = ref;
 		}
 		else {
-			if (parentItemKey) {
-				var ref = Zotero.Items.getByLibraryAndKey(parentItemKey);
-				noteEditor.parentItem = ref;
+			if (collectionID && collectionID != '' && collectionID != 'undefined') {
+				noteEditor.collection = Zotero.Collections.get(collectionID);
 			}
-			else {
-				if (collectionID && collectionID != '' && collectionID != 'undefined') {
-					noteEditor.collection = Zotero.Collections.get(collectionID);
-				}
-			}
-			noteEditor.refresh();
 		}
-		
-		notifierUnregisterID = Zotero.Notifier.registerObserver(NotifyCallback, 'item');
-	});
+		noteEditor.refresh();
+	}
+	
+	noteEditor.focus();
+	notifierUnregisterID = Zotero.Notifier.registerObserver(NotifyCallback, 'item', 'noteWindow');
 }
 
 // If there's an error saving a note, close the window and crash the app
@@ -86,22 +74,20 @@ function onError() {
 	window.close();
 }
 
-function onUnload()
-{
-	if(noteEditor && noteEditor.value)
-		noteEditor.save();
-	
+
+function onUnload() {
 	Zotero.Notifier.unregisterObserver(notifierUnregisterID);
+	
+	if (noteEditor.item) {
+		window.opener.ZoteroPane.onNoteWindowClosed(noteEditor.item.id, noteEditor.value);
+	}
 }
 
 var NotifyCallback = {
 	notify: function(action, type, ids){
-		if (noteEditor.item && ids.indexOf(noteEditor.item.id) != -1) {
-			// If the document title hasn't yet been set, reset undo so
-			// undoing to empty isn't possible
-			var noteTitle = noteEditor.note.getNoteTitle();
+		if (noteEditor.item && ids.includes(noteEditor.item.id)) {
+			var noteTitle = noteEditor.item.getNoteTitle();
 			if (!document.title && noteTitle != '') {
-				noteEditor.clearUndo();
 				document.title = noteTitle;
 			}
 			

chrome/content/zotero/note.xul

@@ -15,7 +15,6 @@
     xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul">
 
 	<script src="include.js"/>
-	<script src="itemPane.js"/>
 	<script src="note.js"/>
 
 	<keyset>

chrome/content/zotero/preferences/preferences_advanced.js

@@ -42,6 +42,28 @@ Zotero_Preferences.Advanced = {
 	},
 	
 	
+	updateTranslators: Zotero.Promise.coroutine(function* () {
+		var updated = yield Zotero.Schema.updateFromRepository(Zotero.Schema.REPO_UPDATE_MANUAL);
+		var button = document.getElementById('updateButton');
+		if (button) {
+			if (updated===-1) {
+				var label = Zotero.getString('zotero.preferences.update.upToDate');
+			}
+			else if (updated) {
+				var label = Zotero.getString('zotero.preferences.update.updated');
+			}
+			else {
+				var label = Zotero.getString('zotero.preferences.update.error');
+			}
+			button.setAttribute('label', label);
+			
+			if (updated && Zotero_Preferences.Cite) {
+				yield Zotero_Preferences.Cite.refreshStylesList();
+			}
+		}
+	}),
+	
+	
 	migrateDataDirectory: Zotero.Promise.coroutine(function* () {
 		var currentDir = Zotero.DataDirectory.dir;
 		var defaultDir = Zotero.DataDirectory.defaultDir;
@@ -133,78 +155,84 @@ Zotero_Preferences.Advanced = {
 	}),
 	
 	
-	runIntegrityCheck: Zotero.Promise.coroutine(function* () {
-		var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
-			.getService(Components.interfaces.nsIPromptService);
+	runIntegrityCheck: async function (button) {
+		button.disabled = true;
 		
-		var ok = yield Zotero.DB.integrityCheck();
-		if (ok) {
-			ok = yield Zotero.Schema.integrityCheck();
-			if (!ok) {
-				var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_IS_STRING)
-					+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_CANCEL);
-				var index = ps.confirmEx(window,
-					Zotero.getString('general.failed'),
-					Zotero.getString('db.integrityCheck.failed') + "\n\n" +
-						Zotero.getString('db.integrityCheck.repairAttempt') + " " +
-						Zotero.getString('db.integrityCheck.appRestartNeeded', Zotero.appName),
-					buttonFlags,
-					Zotero.getString('db.integrityCheck.fixAndRestart', Zotero.appName),
-					null, null, null, {}
-				);
-				
-				if (index == 0) {
-					// Safety first
-					yield Zotero.DB.backupDatabase();
-					
-					// Fix the errors
-					yield Zotero.Schema.integrityCheck(true);
-					
-					// And run the check again
-					ok = yield Zotero.Schema.integrityCheck();
-					var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_IS_STRING);
-					if (ok) {
-						var str = 'success';
-						var msg = Zotero.getString('db.integrityCheck.errorsFixed');
-					}
-					else {
-						var str = 'failed';
-						var msg = Zotero.getString('db.integrityCheck.errorsNotFixed')
-									+ "\n\n" + Zotero.getString('db.integrityCheck.reportInForums');
-					}
-					
-					ps.confirmEx(window,
-						Zotero.getString('general.' + str),
-						msg,
+		try {
+			let ps = Services.prompt;
+			
+			var ok = await Zotero.DB.integrityCheck();
+			if (ok) {
+				ok = await Zotero.Schema.integrityCheck();
+				if (!ok) {
+					var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_IS_STRING)
+						+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_CANCEL);
+					var index = ps.confirmEx(window,
+						Zotero.getString('general.failed'),
+						Zotero.getString('db.integrityCheck.failed') + "\n\n" +
+							Zotero.getString('db.integrityCheck.repairAttempt') + " " +
+							Zotero.getString('db.integrityCheck.appRestartNeeded', Zotero.appName),
 						buttonFlags,
-						Zotero.getString('general.restartApp', Zotero.appName),
+						Zotero.getString('db.integrityCheck.fixAndRestart', Zotero.appName),
 						null, null, null, {}
 					);
 					
-					var appStartup = Components.classes["@mozilla.org/toolkit/app-startup;1"]
-							.getService(Components.interfaces.nsIAppStartup);
-					appStartup.quit(Components.interfaces.nsIAppStartup.eAttemptQuit
-						| Components.interfaces.nsIAppStartup.eRestart);
+					if (index == 0) {
+						// Safety first
+						await Zotero.DB.backupDatabase();
+						
+						// Fix the errors
+						await Zotero.Schema.integrityCheck(true);
+						
+						// And run the check again
+						ok = await Zotero.Schema.integrityCheck();
+						var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_IS_STRING);
+						if (ok) {
+							var str = 'success';
+							var msg = Zotero.getString('db.integrityCheck.errorsFixed');
+						}
+						else {
+							var str = 'failed';
+							var msg = Zotero.getString('db.integrityCheck.errorsNotFixed')
+										+ "\n\n" + Zotero.getString('db.integrityCheck.reportInForums');
+						}
+						
+						ps.confirmEx(window,
+							Zotero.getString('general.' + str),
+							msg,
+							buttonFlags,
+							Zotero.getString('general.restartApp', Zotero.appName),
+							null, null, null, {}
+						);
+						
+						var appStartup = Components.classes["@mozilla.org/toolkit/app-startup;1"]
+								.getService(Components.interfaces.nsIAppStartup);
+						appStartup.quit(Components.interfaces.nsIAppStartup.eAttemptQuit
+							| Components.interfaces.nsIAppStartup.eRestart);
+					}
+					
+					return;
 				}
 				
-				return;
+				try {
+					await Zotero.DB.vacuum();
+				}
+				catch (e) {
+					Zotero.logError(e);
+					ok = false;
+				}
 			}
+			var str = ok ? 'passed' : 'failed';
 			
-			try {
-				yield Zotero.DB.vacuum();
-			}
-			catch (e) {
-				Zotero.logError(e);
-				ok = false;
-			}
+			ps.alert(window,
+				Zotero.getString('general.' + str),
+				Zotero.getString('db.integrityCheck.' + str)
+				+ (!ok ? "\n\n" + Zotero.getString('db.integrityCheck.dbRepairTool') : ''));
 		}
-		var str = ok ? 'passed' : 'failed';
-		
-		ps.alert(window,
-			Zotero.getString('general.' + str),
-			Zotero.getString('db.integrityCheck.' + str)
-			+ (!ok ? "\n\n" + Zotero.getString('db.integrityCheck.dbRepairTool') : ''));
-	}),
+		finally {
+			button.disabled = false;
+		}
+	},
 	
 	
 	resetTranslatorsAndStyles: function () {

chrome/content/zotero/preferences/preferences_advanced.xul

@@ -37,12 +37,16 @@
 			onpaneload="Zotero_Preferences.Advanced.init()"
 			helpTopic="advanced">
 		<preferences>
+			<preference id="pref-automaticScraperUpdates" name="extensions.zotero.automaticScraperUpdates" type="bool"/>
+			<preference id="pref-reportTranslationFailure" name="extensions.zotero.reportTranslationFailure" type="bool"/>
+			
 			<preference id="pref-baseAttachmentPath" name="extensions.zotero.baseAttachmentPath" type="string"/>
 			<preference id="pref-useDataDir" name="extensions.zotero.useDataDir" type="bool"/>
 			<preference id="pref-dataDir" name="extensions.zotero.dataDir" type="string"/>
 			<preference id="pref-debug-output-enableAfterRestart" name="extensions.zotero.debug.store" type="bool"/>
 			<preference id="pref-openURL-resolver" name="extensions.zotero.openURL.resolver" type="string"/>
 			<preference id="pref-openURL-version" name="extensions.zotero.openURL.version" type="string"/>
+			
 			<preference id="pref-keys-openZotero" name="extensions.zotero.keys.openZotero" type="string"/>
 			<preference id="pref-keys-saveToZotero" name="extensions.zotero.keys.saveToZotero" type="string"/>
 			<preference id="pref-keys-library" name="extensions.zotero.keys.library" type="string"/>
@@ -74,6 +78,14 @@
 					<groupbox id="zotero-prefpane-advanced-miscellaneous">
 						<caption label="&zotero.preferences.miscellaneous;"/>
 						
+						<hbox align="center">
+							<checkbox label="&zotero.preferences.autoUpdate;" preference="pref-automaticScraperUpdates"/>
+							<button id="updateButton" style="margin-top:0" label="&zotero.preferences.updateNow;"
+								oncommand="Zotero_Preferences.Advanced.updateTranslators()"/>
+						</hbox>
+						
+						<checkbox label="&zotero.preferences.reportTranslationFailure;" preference="pref-reportTranslationFailure"/>
+						
 						<hbox align="center">
 							<label value="&zotero.bibliography.locale.label;"/>
 							<menulist id="locale-menu"
@@ -202,7 +214,7 @@
 						
 						<hbox style="display: block">
 							<button label="&zotero.preferences.dbMaintenance.integrityCheck;"
-								oncommand="Zotero_Preferences.Advanced.runIntegrityCheck()"/>
+								oncommand="Zotero_Preferences.Advanced.runIntegrityCheck(this)"/>
 							<button id="reset-translators-button"
 								label="&zotero.preferences.dbMaintenance.resetTranslators;"
 								oncommand="Zotero_Preferences.Advanced.resetTranslators()"/>

chrome/content/zotero/preferences/preferences_cite.js

@@ -26,24 +26,50 @@
 "use strict";
 
 Zotero_Preferences.Cite = {
+	wordPluginIDs: new Set([
+		'zoteroOpenOfficeIntegration@zotero.org',
+		'zoteroMacWordIntegration@zotero.org',
+		'zoteroWinWordIntegration@zotero.org'
+	]),
+
 	init: Zotero.Promise.coroutine(function* () {
+		Components.utils.import("resource://gre/modules/AddonManager.jsm");
 		this.updateWordProcessorInstructions();
 		yield this.refreshStylesList();
 	}),
 	
 	
 	/**
-	 * Determines if there are word processors, and if not, enables no word processor message
+	 * Determines if any word processors are disabled and if so, shows a message in the pref pane
 	 */
-	updateWordProcessorInstructions: function () {
-		if(document.getElementById("wordProcessors").childNodes.length == 2) {
-			document.getElementById("wordProcessors-noWordProcessorPluginsInstalled").hidden = undefined;
-		}
-		if(Zotero.isStandalone) {
-			document.getElementById("wordProcessors-getWordProcessorPlugins").hidden = true;
+	updateWordProcessorInstructions: async function () {
+		var someDisabled = false;
+		await new Promise(function(resolve) {
+			AddonManager.getAllAddons(function(addons) {
+				for (let addon of addons) {
+					if (Zotero_Preferences.Cite.wordPluginIDs.has(addon.id) && addon.userDisabled) {
+						someDisabled = true;
+					}
+				}
+				resolve();
+			});
+		});
+		if (someDisabled) {
+			document.getElementById("wordProcessors-somePluginsDisabled").hidden = undefined;
 		}
 	},
 	
+	enableWordPlugins: function () {
+		AddonManager.getAllAddons(function(addons) {
+			for (let addon of addons) {
+				if (Zotero_Preferences.Cite.wordPluginIDs.has(addon.id) && addon.userDisabled) {
+					addon.userDisabled = false;
+				}
+			}
+			return Zotero.Utilities.Internal.quit(true);
+		});
+	},
+	
 	
 	/**
 	 * Refreshes the list of styles in the styles pane

chrome/content/zotero/preferences/preferences_cite.xul

@@ -96,11 +96,15 @@
 					</groupbox>
 				</tabpanel>
 				<tabpanel orient="vertical" id="wordProcessors">
-					<label id="wordProcessors-noWordProcessorPluginsInstalled" width="45em" hidden="true">
-							&zotero.preferences.cite.wordProcessors.noWordProcessorPluginsInstalled;
-					</label>
+					<vbox id="wordProcessors-somePluginsDisabled" hidden="true">
+						<label style="font-weight: bold; margin-top: 1em; text-align: center">Some word processor plugins are disabled.</label>
+						<hbox pack="center" style="margin-bottom: 2em">
+							<button id="wordProcessors-enablePlugins"
+								label="Enable Plugins and Restart Zotero"
+								oncommand="Zotero_Preferences.Cite.enableWordPlugins()"/>
+						</hbox>
+					</vbox>
 					<checkbox label="&zotero.preferences.cite.wordProcessors.useClassicAddCitationDialog;" preference="pref-cite-useClassicAddCitationDialog"/>
-					<label id="wordProcessors-getWordProcessorPlugins" class="zotero-text-link" href="&zotero.preferences.cite.wordProcessors.getPlugins.url;" value="&zotero.preferences.cite.wordProcessors.getPlugins;"/>
 				</tabpanel>
 			</tabpanels>
 		</tabbox>

chrome/content/zotero/preferences/preferences_general.js

@@ -25,6 +25,9 @@
 
 "use strict";
 
+Components.utils.import("resource://gre/modules/Services.jsm");
+Components.utils.import("resource://gre/modules/osfile.jsm");
+
 Zotero_Preferences.General = {
 	init: function () {
 		// JS-based strings
@@ -36,27 +39,89 @@ Zotero_Preferences.General = {
 		}
 		
 		document.getElementById('noteFontSize').value = Zotero.Prefs.get('note.fontSize');
+		
+		this._updateFileHandlerUI();
 	},
 	
+	//
+	// File handlers
+	//
+	chooseFileHandler: function (type) {
+		var pref = this._getFileHandlerPref(type);
+		var currentPath = Zotero.Prefs.get(pref);
+		
+		var nsIFilePicker = Components.interfaces.nsIFilePicker;
+		var fp = Components.classes["@mozilla.org/filepicker;1"]
+			.createInstance(nsIFilePicker);
+		if (currentPath) {
+			fp.displayDirectory = Zotero.File.pathToFile(OS.Path.dirname(currentPath));
+		}
+		fp.init(
+			window,
+			Zotero.getString('zotero.preferences.chooseApplication'),
+			nsIFilePicker.modeOpen
+		);
+		fp.appendFilters(nsIFilePicker.filterApps);
+		if (fp.show() != nsIFilePicker.returnOK) {
+			this._updateFileHandlerUI();
+			return false;
+		}
+		var newPath = OS.Path.normalize(fp.file.path);
+		this.setFileHandler(type, newPath);
+	},
 	
-	updateTranslators: Zotero.Promise.coroutine(function* () {
-		var updated = yield Zotero.Schema.updateFromRepository(Zotero.Schema.REPO_UPDATE_MANUAL);
-		var button = document.getElementById('updateButton');
-		if (button) {
-			if (updated===-1) {
-				var label = Zotero.getString('zotero.preferences.update.upToDate');
+	setFileHandler: function (type, handler) {
+		var pref = this._getFileHandlerPref(type);
+		if (handler) {
+			Zotero.Prefs.set(pref, handler);
+		}
+		else {
+			Zotero.Prefs.clear(pref);
+		}
+		this._updateFileHandlerUI();
+	},
+	
+	_updateFileHandlerUI: function () {
+		var handler = Zotero.Prefs.get('fileHandler.pdf');
+		var menulist = document.getElementById('fileHandler-pdf');
+		var customMenuItem = document.getElementById('fileHandler-custom');
+		if (handler) {
+			let icon;
+			try {
+				let fph = Services.io.getProtocolHandler("file")
+					.QueryInterface(Components.interfaces.nsIFileProtocolHandler);
+				let urlspec = fph.getURLSpecFromFile(Zotero.File.pathToFile(handler));
+				icon = "moz-icon://" + urlspec + "?size=16";
 			}
-			else if (updated) {
-				var label = Zotero.getString('zotero.preferences.update.updated');
+			catch (e) {
+				Zotero.logError(e);
+			}
+			
+			let handlerFilename = OS.Path.basename(handler);
+			if (Zotero.isMac) {
+				handlerFilename = handlerFilename.replace(/\.app$/, '');
+			}
+			customMenuItem.setAttribute('label', handlerFilename);
+			if (icon) {
+				customMenuItem.className = 'menuitem-iconic';
+				customMenuItem.setAttribute('image', icon);
 			}
 			else {
-				var label = Zotero.getString('zotero.preferences.update.error');
-			}
-			button.setAttribute('label', label);
-			
-			if (updated && Zotero_Preferences.Cite) {
-				yield Zotero_Preferences.Cite.refreshStylesList();
+				customMenuItem.className = '';
 			}
+			customMenuItem.hidden = false;
+			menulist.selectedIndex = 0;
 		}
-	})
+		else {
+			customMenuItem.hidden = true;
+			menulist.selectedIndex = 1;
+		}
+	},
+	
+	_getFileHandlerPref: function (type) {
+		if (type != 'pdf') {
+			throw new Error(`Unknown file type ${type}`);
+		}
+		return 'fileHandler.pdf';
+	}
 }

chrome/content/zotero/preferences/preferences_general.xul

@@ -33,10 +33,12 @@
 		<preferences id="zotero-prefpane-general-preferences">
 			<preference id="pref-fontSize" name="extensions.zotero.fontSize" type="string"/>
 			<preference id="pref-layout" name="extensions.zotero.layout" type="string"/>
-			<preference id="pref-automaticScraperUpdates" name="extensions.zotero.automaticScraperUpdates" type="bool"/>
-			<preference id="pref-reportTranslationFailure" name="extensions.zotero.reportTranslationFailure" type="bool"/>
+			
 			<preference id="pref-automaticSnapshots" name="extensions.zotero.automaticSnapshots" type="bool"/>
 			<preference id="pref-downloadAssociatedFiles" name="extensions.zotero.downloadAssociatedFiles" type="bool"/>
+			<preference id="pref-autoRecognizeFiles" name="extensions.zotero.autoRecognizeFiles" type="bool"/>
+			<preference id="pref-autoRenameFiles" name="extensions.zotero.autoRenameFiles" type="bool"/>
+			
 			<preference id="pref-automaticTags" name="extensions.zotero.automaticTags" type="bool"/>
 			<preference id="pref-trashAutoEmptyDays" name="extensions.zotero.trashAutoEmptyDays" type="int"/>
 			
@@ -108,20 +110,33 @@
 			</grid>
 		</groupbox>
 		
-		<groupbox id="zotero-prefpane-miscellaneous-groupbox">
-			<caption label="&zotero.preferences.miscellaneous;"/>
+		<groupbox id="zotero-prefpane-file-handling-groupbox">
+			<caption label="&zotero.preferences.fileHandling;"/>
 			
-			<hbox align="center">
-				<checkbox label="&zotero.preferences.autoUpdate;" preference="pref-automaticScraperUpdates"/>
-				<button id="updateButton" style="margin-top:0" label="&zotero.preferences.updateNow;"
-					oncommand="Zotero_Preferences.General.updateTranslators()"/>
-			</hbox>
-			
-			<checkbox label="&zotero.preferences.reportTranslationFailure;" preference="pref-reportTranslationFailure"/>
 			<checkbox id="automaticSnapshots-checkbox"
 				label="&zotero.preferences.automaticSnapshots;"
 				preference="pref-automaticSnapshots"/>
 			<checkbox label="&zotero.preferences.downloadAssociatedFiles;" preference="pref-downloadAssociatedFiles"/>
+			<checkbox label="&zotero.preferences.autoRecognizeFiles;" preference="pref-autoRecognizeFiles"/>
+			<checkbox label="&zotero.preferences.autoRenameFiles;" preference="pref-autoRenameFiles"/>
+			
+			<hbox align="center">
+				<label value="&zotero.preferences.fileHandler.openPDFsUsing;" control="file-handler-pdf"/>
+				<menulist id="fileHandler-pdf" class="fileHandler-menu">
+					<menupopup>
+						<menuitem id="fileHandler-custom"/>
+						<menuitem label="&zotero.preferences.fileHandler.systemDefault;"
+								oncommand="Zotero_Preferences.General.setFileHandler('pdf', false)"/>
+						<menuitem label="&zotero.preferences.custom;"
+								oncommand="Zotero_Preferences.General.chooseFileHandler('pdf')"/>
+					</menupopup>
+				</menulist>
+			</hbox>
+		</groupbox>
+		
+		<groupbox id="zotero-prefpane-miscellaneous-groupbox">
+			<caption label="&zotero.preferences.miscellaneous;"/>
+			
 			<checkbox label="&zotero.preferences.automaticTags;" preference="pref-automaticTags"/>
 			<hbox align="center">
 				<label value="&zotero.preferences.trashAutoEmptyDaysPre;"/>

chrome/content/zotero/preferences/preferences_search.js

@@ -33,264 +33,10 @@ Zotero_Preferences.Search = {
 		document.getElementById('fulltext-clearIndex').setAttribute('label',
 			Zotero.getString('zotero.preferences.search.clearIndex')
 				+ Zotero.getString('punctuation.ellipsis'));
-		this.updatePDFToolsStatus();
 		
 		this.updateIndexStats();
-		
-		// Quick hack to support install prompt from PDF recognize option
-		var io = window.arguments[0];
-		if (io.action && io.action == 'pdftools-install') {
-			this.checkPDFToolsDownloadVersion();
-		}
 	},
 	
-	/*
-	 * Update window according to installation status for PDF tools
-	 *  (e.g. status line, install/update button, etc.)
-	 */
-	updatePDFToolsStatus: function () {
-		var converterIsRegistered = Zotero.Fulltext.pdfConverterIsRegistered();
-		var infoIsRegistered = Zotero.Fulltext.pdfInfoIsRegistered();
-		
-		var converterStatusLabel = document.getElementById('pdfconverter-status');
-		var infoStatusLabel = document.getElementById('pdfinfo-status');
-		var requiredLabel = document.getElementById('pdftools-required');
-		var updateButton = document.getElementById('pdftools-update-button');
-		var documentationLink = document.getElementById('pdftools-documentation-link');
-		var settingsBox = document.getElementById('pdftools-settings');
-		
-		// If we haven't already generated the required and documentation messages
-		if (!converterIsRegistered && !requiredLabel.hasChildNodes()) {
-			
-			// Xpdf link
-			var str = Zotero.getString('zotero.preferences.search.pdf.toolsRequired',
-				[Zotero.Fulltext.pdfConverterName, Zotero.Fulltext.pdfInfoName,
-				'<a href="' + Zotero.Fulltext.pdfToolsURL + '">'
-				+ Zotero.Fulltext.pdfToolsName + '</a>']);
-			var parts = Zotero.Utilities.parseMarkup(str);
-			for (var i=0; i<parts.length; i++) {
-				var part = parts[i];
-				if (part.type == 'text') {
-					var elem = document.createTextNode(part.text);
-				}
-				else if (part.type == 'link') {
-					var elem = document.createElement('label');
-					elem.setAttribute('value', part.text);
-					elem.setAttribute('class', 'zotero-text-link');
-					for (var key in part.attributes) {
-						elem.setAttribute(key, part.attributes[key]);
-						
-						if (key == 'href') {
-							elem.setAttribute('tooltiptext', part.attributes[key]);
-						}
-					}
-				}
-				requiredLabel.appendChild(elem);
-			}
-			
-			requiredLabel.appendChild(document.createTextNode(' '
-				+ Zotero.getString('zotero.preferences.search.pdf.automaticInstall')));
-			
-			// Documentation link
-			var link = '<a href="http://www.zotero.org/documentation/pdf_fulltext_indexing">'
-				+ Zotero.getString('zotero.preferences.search.pdf.documentationLink')
-				+ '</a>';
-			var str = Zotero.getString('zotero.preferences.search.pdf.advancedUsers', link);
-			var parts = Zotero.Utilities.parseMarkup(str);
-			
-			for (var i=0; i<parts.length; i++) {
-				var part = parts[i];
-				if (part.type == 'text') {
-					var elem = document.createTextNode(part.text);
-				}
-				else if (part.type == 'link') {
-					var elem = document.createElement('label');
-					elem.setAttribute('value', part.text);
-					elem.setAttribute('class', 'zotero-text-link');
-					for (var key in part.attributes) {
-						elem.setAttribute(key, part.attributes[key]);
-						
-						if (key == 'href') {
-							elem.setAttribute('tooltiptext', part.attributes[key]);
-						}
-					}
-				}
-				documentationLink.appendChild(elem);
-			}
-		}
-		
-		// converter status line
-		var prefix = 'zotero.preferences.search.pdf.tool';
-		if (converterIsRegistered) {
-			var version = Zotero.Fulltext.pdfConverterVersion;
-			str = Zotero.getString(prefix + 'Registered',
-				Zotero.getString('zotero.preferences.search.pdf.toolVersionPlatform',
-					[Zotero.Fulltext.pdfConverterName, version]));
-		}
-		else {
-			str = Zotero.getString(prefix + 'NotRegistered',
-				[Zotero.Fulltext.pdfConverterFileName]);
-		}
-		converterStatusLabel.setAttribute('value', str);
-		
-		// pdfinfo status line
-		if (infoIsRegistered) {
-			var version = Zotero.Fulltext.pdfInfoVersion;
-			str = Zotero.getString(prefix + 'Registered',
-				Zotero.getString('zotero.preferences.search.pdf.toolVersionPlatform',
-					[Zotero.Fulltext.pdfInfoName, version]));
-		}
-		else {
-			str = Zotero.getString(prefix + 'NotRegistered',
-				[Zotero.Fulltext.pdfInfoFileName]);
-		}
-		infoStatusLabel.setAttribute('value', str);
-		
-		str = converterIsRegistered ?
-			Zotero.getString('general.checkForUpdate') :
-			Zotero.getString('zotero.preferences.search.pdf.checkForInstaller');
-		updateButton.setAttribute('label', str);
-		
-		requiredLabel.setAttribute('hidden', converterIsRegistered);
-		documentationLink.setAttribute('hidden', converterIsRegistered);
-		settingsBox.setAttribute('hidden', !converterIsRegistered);
-	},
-	
-	
-	/*
-	 * Check available versions of PDF tools from server and prompt for installation
-	 * if a newer version is available
-	 */
-	checkPDFToolsDownloadVersion: Zotero.Promise.coroutine(function* () {
-		try {
-			var latestVersion = yield Zotero.Fulltext.getLatestPDFToolsVersion();
-			
-			var converterIsRegistered = Zotero.Fulltext.pdfConverterIsRegistered();
-			var infoIsRegistered = Zotero.Fulltext.pdfInfoIsRegistered();
-			var bothRegistered = converterIsRegistered && infoIsRegistered;
-			
-			// On Windows, install if not installed or anything other than 3.02a
-			if (Zotero.isWin) {
-				var converterVersionAvailable = !converterIsRegistered
-					|| Zotero.Fulltext.pdfConverterVersion != '3.02a';
-				var infoVersionAvailable = !infoIsRegistered
-					|| Zotero.Fulltext.pdfInfoVersion != '3.02a';
-				var bothAvailable = converterVersionAvailable && infoVersionAvailable;
-			}
-			// Install if not installed, version unknown, outdated, or
-			// Xpdf 3.02/3.04 (to upgrade to Poppler),
-			else {
-				var converterVersionAvailable = (!converterIsRegistered ||
-						Zotero.Fulltext.pdfConverterVersion == 'UNKNOWN'
-							|| latestVersion > Zotero.Fulltext.pdfConverterVersion
-							|| (!latestVersion.startsWith('3.02')
-								&& Zotero.Fulltext.pdfConverterVersion.startsWith('3.02'))
-							|| (!latestVersion.startsWith('3.02') && latestVersion != '3.04'
-								&& Zotero.Fulltext.pdfConverterVersion == '3.04'));
-				var infoVersionAvailable = (!infoIsRegistered ||
-						Zotero.Fulltext.pdfInfoVersion == 'UNKNOWN'
-							|| latestVersion > Zotero.Fulltext.pdfInfoVersion
-							|| (!latestVersion.startsWith('3.02')
-								&& Zotero.Fulltext.pdfInfoVersion.startsWith('3.02'))
-							|| (!latestVersion.startsWith('3.02') && latestVersion != '3.04'
-								&& Zotero.Fulltext.pdfInfoVersion == '3.04'));
-				var bothAvailable = converterVersionAvailable && infoVersionAvailable;
-			}
-			
-			// Up to date -- disable update button
-			if (!converterVersionAvailable && !infoVersionAvailable) {
-				var button = document.getElementById('pdftools-update-button');
-				button.setAttribute('label', Zotero.getString('zotero.preferences.update.upToDate'));
-				button.setAttribute('disabled', true);
-				return;
-			}
-			
-			// New version available -- display update prompt
-			var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"].
-					createInstance(Components.interfaces.nsIPromptService);
-			var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_IS_STRING)
-				+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_CANCEL);
-			
-			var msg = Zotero.getString('zotero.preferences.search.pdf.available'
-				+ ((converterIsRegistered || infoIsRegistered) ? 'Updates' : 'Downloads'),
-				[Zotero.platform, 'zotero.org']) + '\n\n';
-			
-			if (converterVersionAvailable) {
-				let tvp = Zotero.getString('zotero.preferences.search.pdf.toolVersionPlatform',
-					[Zotero.Fulltext.pdfConverterName, latestVersion]);
-				msg += '- ' + tvp + '\n';
-			}
-			if (infoVersionAvailable) {
-				let tvp = Zotero.getString('zotero.preferences.search.pdf.toolVersionPlatform',
-					[Zotero.Fulltext.pdfInfoName, latestVersion]);
-				msg += '- ' + tvp + '\n';
-			}
-			msg += '\n';
-			msg += Zotero.getString('zotero.preferences.search.pdf.zoteroCanInstallVersion'
-					+ (bothAvailable ? 's' : ''));
-			
-			var index = ps.confirmEx(null,
-				converterIsRegistered ?
-					Zotero.getString('general.updateAvailable') : '',
-				msg,
-				buttonFlags,
-				converterIsRegistered ?
-					Zotero.getString('general.upgrade') :
-					Zotero.getString('general.install'),
-				null, null, null, {});
-			
-			if (index != 0) {
-				return;
-			}
-			
-			document.getElementById('pdftools-update-button').disabled = true;
-			var str = Zotero.getString('zotero.preferences.search.pdf.downloading');
-			document.getElementById('pdftools-update-button').setAttribute('label', str);
-			
-			if (converterVersionAvailable) {
-				yield Zotero.Fulltext.downloadPDFTool('converter', latestVersion)
-				.catch(function (e) {
-					Zotero.logError(e);
-					throw new Error("Error downloading pdftotext");
-				});
-			}
-			if (infoVersionAvailable) {
-				yield Zotero.Fulltext.downloadPDFTool('info', latestVersion)
-				.catch(function (e) {
-					Zotero.logError(e);
-					throw new Error("Error downloading pdfinfo");
-				});
-			}
-			this.updatePDFToolsStatus();
-		}
-		catch (e) {
-			this.onPDFToolsDownloadError(e);
-		}
-	}),
-	
-	
-	onPDFToolsDownloadError: function (e) {
-		if (e == 404) {
-			var str = Zotero.getString('zotero.preferences.search.pdf.toolDownloadsNotAvailable',
-				Zotero.Fulltext.pdfToolsName) + ' '
-				+ Zotero.getString('zotero.preferences.search.pdf.viewManualInstructions');
-		}
-		else {
-			Components.utils.reportError(e);
-			var str = Zotero.getString('zotero.preferences.search.pdf.toolsDownloadError', Zotero.Fulltext.pdfToolsName)
-				+ ' ' + Zotero.getString('zotero.preferences.search.pdf.tryAgainOrViewManualInstructions');
-		}
-		
-		var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
-			.createInstance(Components.interfaces.nsIPromptService);
-		ps.alert(
-			null,
-			Zotero.getString('pane.item.attachments.PDF.installTools.title'),
-			str
-		);
-	},
-	
-	
 	updateIndexStats: Zotero.Promise.coroutine(function* () {
 		var stats = yield Zotero.Fulltext.getIndexStats();
 		document.getElementById('fulltext-stats-indexed').

chrome/content/zotero/preferences/preferences_search.xul

@@ -49,34 +49,10 @@
 				<textbox size="10" preference="pref-fulltext-textMaxLength"/>
 				<label value="(&zotero.preferences.default; 500000)"/>
 			</hbox>
-		</groupbox>
-		
-		<groupbox id="pdftools-box">
-			<caption label="&zotero.preferences.search.pdfIndexing;"/>
-			
-			<label id="pdfconverter-status"/>
+
 			<separator class="thin"/>
-			<label id="pdfinfo-status"/>
-			
-			<separator class="thin"/>
-			
-			<!-- This doesn't wrap without an explicit width -->
-			<label id="pdftools-required" width="45em" hidden="true"/>
-			
-			<separator class="thin"/>
-			
-			<hbox>
-				<button id="pdftools-update-button" flex="1" oncommand="Zotero_Preferences.Search.checkPDFToolsDownloadVersion()"/>
-			</hbox>
-			
-			<separator class="thin"/>
-			
-			<!-- This doesn't wrap without an explicit width -->
-			<label id="pdftools-documentation-link" width="45em" hidden="true"/>
-			
-			<separator class="thin"/>
-			
-			<hbox id="pdftools-settings" align="center" hidden="true">
+
+			<hbox align="center">
 				<label value="&zotero.preferences.fulltext.pdfMaxPages;"/>
 				<textbox size="5" preference="pref-fulltext-pdfmaxpages"/>
 				<label value="(&zotero.preferences.default; 100)"/>

chrome/content/zotero/preferences/preferences_sync.js

@@ -26,10 +26,12 @@
 "use strict";
 Components.utils.import("resource://gre/modules/Services.jsm");
 Components.utils.import("resource://gre/modules/osfile.jsm");
+Components.utils.import("resource://zotero/config.js");
 
 Zotero_Preferences.Sync = {
 	init: Zotero.Promise.coroutine(function* () {
 		this.updateStorageSettingsUI();
+		this.updateStorageSettingsGroupsUI();
 
 		var username = Zotero.Users.getCurrentUsername() || Zotero.Prefs.get('sync.server.username') || " ";
 		var apiKey = yield Zotero.Sync.Data.Local.getAPIKey();
@@ -63,8 +65,10 @@ Zotero_Preferences.Sync = {
 				}
 			}
 		}
+		
+		this.initResetPane();
 	}),
-
+	
 	displayFields: function (username) {
 		document.getElementById('sync-unauthorized').hidden = !!username;
 		document.getElementById('sync-authorized').hidden = !username;
@@ -365,30 +369,19 @@ Zotero_Preferences.Sync = {
 			sep.hidden = true;
 		}
 		
-		var menulists = document.querySelectorAll('#storage-settings menulist.storage-mode');
-		for (let menulist of menulists) {
-			menulist.disabled = !enabled;
-		}
-		
+		document.getElementById('storage-user-download-mode').disabled = !enabled;
 		this.updateStorageTerms();
 		
 		window.sizeToContent();
 	}),
 	
 	
-	updateStorageSettingsGroups: function (enabled) {
-		var storageSettings = document.getElementById('storage-settings');
-		var menulists = storageSettings.getElementsByTagName('menulist');
-		for (let menulist of menulists) {
-			if (menulist.className == 'storage-groups') {
-				menulist.disabled = !enabled;
-			}
-		}
-		
-		var self = this;
-		setTimeout(function () {
-			self.updateStorageTerms();
-		}, 1)
+	updateStorageSettingsGroupsUI: function () {
+		setTimeout(() => {
+			var enabled = document.getElementById('pref-storage-groups-enabled').value;
+			document.getElementById('storage-groups-download-mode').disabled = !enabled;
+			this.updateStorageTerms();
+		});
 	},
 	
 	
@@ -397,7 +390,7 @@ Zotero_Preferences.Sync = {
 		
 		var libraryEnabled = document.getElementById('pref-storage-enabled').value;
 		var storageProtocol = document.getElementById('pref-storage-protocol').value;
-		var groupsEnabled = document.getElementById('pref-group-storage-enabled').value;
+		var groupsEnabled = document.getElementById('pref-storage-groups-enabled').value;
 		
 		terms.hidden = !((libraryEnabled && storageProtocol == 'zotero') || groupsEnabled);
 	},
@@ -405,7 +398,6 @@ Zotero_Preferences.Sync = {
 	
 	onStorageSettingsKeyPress: Zotero.Promise.coroutine(function* (event) {
 		if (event.keyCode == 13) {
-			yield this.onStorageSettingsChange();
 			yield this.verifyStorageServer();
 		}
 	}),
@@ -425,7 +417,7 @@ Zotero_Preferences.Sync = {
 		var newEnabled = document.getElementById('pref-storage-enabled').value;
 		
 		if (oldProtocol != newProtocol) {
-			yield Zotero.Sync.Storage.Local.resetAllSyncStates();
+			yield Zotero.Sync.Storage.Local.resetAllSyncStates(Zotero.Libraries.userLibraryID);
 		}
 		
 		if (oldProtocol == 'webdav') {
@@ -487,6 +479,11 @@ Zotero_Preferences.Sync = {
 	
 	
 	verifyStorageServer: Zotero.Promise.coroutine(function* () {
+		// onchange weirdly isn't triggered when clicking straight from a field to the button,
+		// so we have to trigger this here (and we don't trigger it for Enter in
+		// onStorageSettingsKeyPress()).
+		yield this.onStorageSettingsChange();
+		
 		Zotero.debug("Verifying storage");
 		
 		var verifyButton = document.getElementById("storage-verify");
@@ -570,38 +567,87 @@ Zotero_Preferences.Sync = {
 	},
 	
 	
-	handleSyncResetSelect: function (obj) {
-		var index = obj.selectedIndex;
-		var rows = obj.getElementsByTagName('row');
+	//
+	// Reset pane
+	//
+	initResetPane: function () {
+		//
+		// Build library selector
+		//
+		var libraryMenu = document.getElementById('sync-reset-library-menu');
+		// Some options need to be disabled when certain libraries are selected
+		libraryMenu.onchange = (event) => {
+			this.onResetLibraryChange(parseInt(event.target.value));
+		}
+		this.onResetLibraryChange(Zotero.Libraries.userLibraryID);
+		var libraries = Zotero.Libraries.getAll()
+			.filter(x => x.libraryType == 'user' || x.libraryType == 'group');
+		Zotero.Utilities.Internal.buildLibraryMenuHTML(libraryMenu, libraries);
+		// Disable read-only libraries, at least until there are options that make sense for those
+		Array.from(libraryMenu.querySelectorAll('option'))
+			.filter(x => x.getAttribute('data-editable') == 'false')
+			.forEach(x => x.disabled = true);
 		
-		for (var i=0; i<rows.length; i++) {
-			if (i == index) {
-				rows[i].setAttribute('selected', 'true');
-			}
-			else {
-				rows[i].removeAttribute('selected');
-			}
+		var list = document.getElementById('sync-reset-list');
+		for (let li of document.querySelectorAll('#sync-reset-list li')) {
+			li.addEventListener('click', function (event) {
+				// Ignore clicks if disabled
+				if (this.hasAttribute('disabled')) {
+					event.stopPropagation();
+					return;
+				}
+				document.getElementById('sync-reset-button').disabled = false;
+			});
 		}
 	},
 	
 	
-	handleSyncReset: Zotero.Promise.coroutine(function* (action) {
-		var ps = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
-								.getService(Components.interfaces.nsIPromptService);
+	onResetLibraryChange: function (libraryID) {
+		var library = Zotero.Libraries.get(libraryID);
+		var section = document.getElementById('reset-file-sync-history');
+		var input = section.querySelector('input');
+		if (library.filesEditable) {
+			section.removeAttribute('disabled');
+			input.disabled = false;
+		}
+		else {
+			section.setAttribute('disabled', '');
+			// If radio we're disabling is already selected, select the first one in the list
+			// instead
+			if (input.checked) {
+				document.querySelector('#sync-reset-list li:first-child input').checked = true;
+			}
+			input.disabled = true;
+		}
+	},
+	
+	
+	reset: async function () {
+		var ps = Services.prompt;
 		
-		if (!Zotero.Sync.Runner.enabled) {
-			ps.alert(
+		if (Zotero.Sync.Runner.syncInProgress) {
+			Zotero.alert(
 				null,
 				Zotero.getString('general.error'),
-				Zotero.getString('zotero.preferences.sync.reset.userInfoMissing',
-								document.getElementById('zotero-prefpane-sync')
-								.getElementsByTagName('tab')[0].label)
+				Zotero.getString('sync.error.syncInProgress')
+					+ "\n\n"
+					+ Zotero.getString('general.operationInProgress.waitUntilFinishedAndTryAgain')
 			);
 			return;
 		}
 		
+		var libraryID = parseInt(
+			Array.from(document.querySelectorAll('#sync-reset-library-menu option'))
+				.filter(x => x.selected)[0]
+				.value
+		);
+		var library = Zotero.Libraries.get(libraryID);
+		var action = Array.from(document.querySelectorAll('#sync-reset-list input[name=sync-reset-radiogroup]'))
+			.filter(x => x.checked)[0]
+			.getAttribute('value');
+		
 		switch (action) {
-			case 'full-sync':
+			/*case 'full-sync':
 				var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_IS_STRING)
 					+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_CANCEL)
 					+ ps.BUTTON_POS_1_DEFAULT;
@@ -622,7 +668,7 @@ Zotero_Preferences.Sync = {
 				switch (index) {
 				case 0:
 					let libraries = Zotero.Libraries.getAll().filter(library => library.syncable);
-					yield Zotero.DB.executeTransaction(function* () {
+					await Zotero.DB.executeTransaction(function* () {
 						for (let library of libraries) {
 							library.libraryVersion = -1;
 							yield library.save();
@@ -655,13 +701,13 @@ Zotero_Preferences.Sync = {
 						// TODO: better error handling
 						
 						// Verify username and password
-						var callback = Zotero.Promise.coroutine(function* () {
+						var callback = async function () {
 							Zotero.Schema.stopRepositoryTimer();
 							Zotero.Sync.Runner.clearSyncTimeout();
 							
 							Zotero.DB.skipBackup = true;
 							
-							yield Zotero.File.putContentsAsync(
+							await Zotero.File.putContentsAsync(
 								OS.Path.join(Zotero.DataDirectory.dir, 'restore-from-server'),
 								''
 							);
@@ -679,7 +725,7 @@ Zotero_Preferences.Sync = {
 							var appStartup = Components.classes["@mozilla.org/toolkit/app-startup;1"]
 									.getService(Components.interfaces.nsIAppStartup);
 							appStartup.quit(Components.interfaces.nsIAppStartup.eRestart | Components.interfaces.nsIAppStartup.eAttemptQuit);
-						});
+						};
 						
 						// TODO: better way of checking for an active session?
 						if (Zotero.Sync.Server.sessionIDComponent == 'sessionid=') {
@@ -696,52 +742,37 @@ Zotero_Preferences.Sync = {
 					case 1:
 						return;
 				}
-				break;
+				break;*/
 			
 			case 'restore-to-server':
 				var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_IS_STRING)
-								+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_CANCEL)
-								+ ps.BUTTON_POS_1_DEFAULT;
+					+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_CANCEL)
+					+ ps.BUTTON_POS_1_DEFAULT;
 				var index = ps.confirmEx(
 					null,
 					Zotero.getString('general.warning'),
-					Zotero.getString('zotero.preferences.sync.reset.restoreToServer', account),
+					Zotero.getString(
+						'zotero.preferences.sync.reset.restoreToServer',
+						[Zotero.clientName, library.name, ZOTERO_CONFIG.DOMAIN_NAME]
+					),
 					buttonFlags,
-					Zotero.getString('zotero.preferences.sync.reset.replaceServerData'),
+					Zotero.getString('zotero.preferences.sync.reset.restoreToServer.button'),
 					null, null, null, {}
 				);
 				
 				switch (index) {
 					case 0:
-						// TODO: better error handling
-						Zotero.Sync.Server.clear(function () {
-							Zotero.Sync.Server.sync(/*{
-								
-								// TODO: this doesn't work if the pref window is 
-								closed. fix, perhaps by making original callbacks
-								available to the custom callbacks
-								
-								onSuccess: function () {
-									Zotero.Sync.Runner.updateIcons();
-									ps.alert(
-										null,
-										"Restore Completed",
-										"Data on the Zotero server has been successfully restored."
-									);
-								},
-								onError: function (msg) {
-									// TODO: combine with error dialog for regular syncs
-									ps.alert(
-										null,
-										"Restore Failed",
-										"An error occurred uploading your data to the server.\n\n"
-											+ "Click the sync error icon in the Zotero toolbar "
-											+ "for further information."
-									);
-									Zotero.Sync.Runner.error(msg);
-								}
-							}*/);
-						});
+						var resetButton = document.getElementById('sync-reset-button');
+						resetButton.disabled = true;
+						try {
+							await Zotero.Sync.Runner.sync({
+								libraries: [libraryID],
+								resetMode: Zotero.Sync.Runner.RESET_MODE_TO_SERVER
+							});
+						}
+						finally {
+							resetButton.disabled = false;
+						}
 						break;
 					
 					// Cancel
@@ -752,14 +783,17 @@ Zotero_Preferences.Sync = {
 				break;
 			
 			
-			case 'reset-storage-history':
-				var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_IS_STRING)
-								+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_CANCEL)
-								+ ps.BUTTON_POS_1_DEFAULT;
+			case 'reset-file-sync-history':
+				var buttonFlags = ps.BUTTON_POS_0 * ps.BUTTON_TITLE_IS_STRING
+					+ ps.BUTTON_POS_1 * ps.BUTTON_TITLE_CANCEL
+					+ ps.BUTTON_POS_1_DEFAULT;
 				var index = ps.confirmEx(
 					null,
 					Zotero.getString('general.warning'),
-					Zotero.getString('zotero.preferences.sync.reset.fileSyncHistory', Zotero.clientName),
+					Zotero.getString(
+						'zotero.preferences.sync.reset.fileSyncHistory',
+						[Zotero.clientName, library.name]
+					),
 					buttonFlags,
 					Zotero.getString('general.reset'),
 					null, null, null, {}
@@ -767,11 +801,14 @@ Zotero_Preferences.Sync = {
 				
 				switch (index) {
 					case 0:
-						yield Zotero.Sync.Storage.Local.resetAllSyncStates();
+						await Zotero.Sync.Storage.Local.resetAllSyncStates(libraryID);
 						ps.alert(
 							null,
-							"File Sync History Cleared",
-							"The file sync history has been cleared."
+							Zotero.getString('general.success'),
+							Zotero.getString(
+								'zotero.preferences.sync.reset.fileSyncHistory.cleared',
+								library.name
+							)
 						);
 						break;
 					
@@ -783,7 +820,7 @@ Zotero_Preferences.Sync = {
 				break;
 			
 			default:
-				throw ("Invalid action '" + action + "' in handleSyncReset()");
+				throw new Error(`Invalid action '${action}' in handleSyncReset()`);
 		}
-	})
+	}
 };

chrome/content/zotero/preferences/preferences_sync.xul

@@ -40,7 +40,7 @@
 			<preference id="pref-storage-username" name="extensions.zotero.sync.storage.username" type="string"/>
 			<preference id="pref-storage-downloadMode-personal" name="extensions.zotero.sync.storage.downloadMode.personal" type="string"/>
 			<preference id="pref-storage-downloadMode-groups" name="extensions.zotero.sync.storage.downloadMode.groups" type="string"/>
-			<preference id="pref-group-storage-enabled" name="extensions.zotero.sync.storage.groups.enabled" type="bool"/>
+			<preference id="pref-storage-groups-enabled" name="extensions.zotero.sync.storage.groups.enabled" type="bool"/>
 		</preferences>
 		
 		<tabbox>
@@ -219,7 +219,7 @@
 									<row>
 										<box/>
 										<hbox>
-											<button id="storage-verify" label="Verify Server"
+											<button id="storage-verify" label="&zotero.preferences.sync.fileSyncing.verifyServer;"
 												oncommand="Zotero_Preferences.Sync.verifyStorageServer()"/>
 											<button id="storage-abort" label="Stop" hidden="true"/>
 											<progressmeter id="storage-progress" hidden="true"
@@ -233,7 +233,10 @@
 
 							<hbox class="storage-settings-download-options" align="center">
 								<label value="&zotero.preferences.sync.fileSyncing.download;"/>
-								<menulist class="storage-mode" preference="pref-storage-downloadMode-personal" style="margin-left: 0">
+								<menulist id="storage-user-download-mode"
+										class="storage-mode"
+										preference="pref-storage-downloadMode-personal"
+										style="margin-left: 0">
 									<menupopup>
 										<menuitem label="&zotero.preferences.sync.fileSyncing.download.onDemand;" value="on-demand"/>
 										<menuitem label="&zotero.preferences.sync.fileSyncing.download.atSyncTime;" value="on-sync"/>
@@ -245,12 +248,15 @@
 
 							<!-- Group Libraries -->
 							<checkbox label="&zotero.preferences.sync.fileSyncing.groups;"
-									preference="pref-group-storage-enabled"
-										oncommand="Zotero_Preferences.Sync.updateStorageSettingsGroups(this.checked)"/>
+									preference="pref-storage-groups-enabled"
+										oncommand="Zotero_Preferences.Sync.updateStorageSettingsGroupsUI()"/>
 
 							<hbox class="storage-settings-download-options" align="center">
 								<label value="&zotero.preferences.sync.fileSyncing.download;"/>
-								<menulist class="storage-mode" preference="pref-storage-downloadMode-groups" style="margin-left: 0">
+								<menulist id="storage-groups-download-mode"
+										class="storage-mode"
+										preference="pref-storage-downloadMode-groups"
+										style="margin-left: 0">
 									<menupopup>
 										<menuitem label="&zotero.preferences.sync.fileSyncing.download.onDemand;" value="on-demand"/>
 										<menuitem label="&zotero.preferences.sync.fileSyncing.download.atSyncTime;" value="on-sync"/>
@@ -260,8 +266,8 @@
 
 							<separator class="thin"/>
 
-							<vbox>
-								<hbox id="storage-terms" style="margin-top: .4em; display: block" align="center">
+							<vbox id="storage-terms">
+								<hbox style="margin-top: .4em; display: block" align="center">
 									<label>&zotero.preferences.sync.fileSyncing.tos1;</label>
 									<label class="zotero-text-link" href="https://www.zotero.org/support/terms/terms_of_service" value="&zotero.preferences.sync.fileSyncing.tos2;"/>
 									<label>&zotero.preferences.period;</label>
@@ -271,82 +277,47 @@
 					</vbox>
 				</tabpanel>
 
-				<tabpanel id="zotero-reset" orient="vertical">
+				<tabpanel id="sync-reset" orient="vertical">
 					<!-- This doesn't wrap without an explicit width, for some reason -->
-					<description width="45em">&zotero.preferences.sync.reset.warning1;<label style="margin-left: 0; margin-right: 0" class="zotero-text-link" href="http://zotero.org/support/kb/sync_reset_options">&zotero.preferences.sync.reset.warning2;</label>&zotero.preferences.sync.reset.warning3;</description>
+					<description id="reset-sync-warning" width="45em">&zotero.preferences.sync.reset.warning1;<label style="margin-left: 0; margin-right: 0" class="zotero-text-link" href="http://zotero.org/support/kb/sync_reset_options">&zotero.preferences.sync.reset.warning2;</label>&zotero.preferences.sync.reset.warning3;</description>
 					
-					<groupbox>
-						<caption label="&zotero.preferences.sync.syncServer;"/>
+					<div id="sync-reset-form" xmlns="http://www.w3.org/1999/xhtml">
+						<div id="sync-reset-library-menu-container">
+							<label>Library: <select id="sync-reset-library-menu"/></label>
+						</div>
 						
-						<radiogroup oncommand="Zotero_Preferences.Sync.handleSyncResetSelect(this)">
-							<grid>
-								<columns>
-									<column/>
-									<column align="start" pack="start" flex="1"/>
-								</columns>
-								
-								<rows id="sync-reset-rows">
-									<!--
-									<row id="zotero-restore-from-server" selected="true">
-										<radio/>
-										<vbox onclick="this.previousSibling.click()">
-											<label value="&zotero.preferences.sync.reset.restoreFromServer;"/>
-											<description>&zotero.preferences.sync.reset.restoreFromServer.desc;</description>
-										</vbox>
-									</row>
-									
-									<row id="zotero-restore-to-server">
-										<radio/>
-										<vbox onclick="this.previousSibling.click()">
-											<label value="&zotero.preferences.sync.reset.restoreToServer;"/>
-											<description>&zotero.preferences.sync.reset.restoreToServer.desc;</description>
-										</vbox>
-									</row>
-									-->
-									<row id="zotero-reset-data-sync-history">
-										<radio hidden="true"/>
-										<vbox onclick="this.previousSibling.click()">
-											<label value="&zotero.preferences.sync.reset.resetDataSyncHistory;"/>
-											<description>&zotero.preferences.sync.reset.resetDataSyncHistory.desc;</description>
-										</vbox>
-									</row>
-								</rows>
-							</grid>
-						</radiogroup>
+						<ul id="sync-reset-list">
+							<!--<li>
+								<p>&zotero.preferences.sync.reset.restoreFromServer;</p>
+								<p>&zotero.preferences.sync.reset.restoreFromServer.desc;</p>
+							</li>-->
+							
+							<li id="restore-to-server">
+								<label>
+									<input name="sync-reset-radiogroup" value="restore-to-server" type="radio"/>
+									<span class="sync-reset-option-name">&zotero.preferences.sync.reset.restoreToServer;</span>
+									<span class="sync-reset-option-desc">&zotero.preferences.sync.reset.restoreToServer.desc;</span>
+								</label>
+							</li>
+							
+							<!--<li>
+								<h2>&zotero.preferences.sync.reset.resetDataSyncHistory;</h2>
+								<description>&zotero.preferences.sync.reset.resetDataSyncHistory.desc;</p>
+							</li>-->
+							
+							<li id="reset-file-sync-history">
+								<label>
+									<input name="sync-reset-radiogroup" value="reset-file-sync-history" type="radio"/>
+									<span class="sync-reset-option-name">&zotero.preferences.sync.reset.resetFileSyncHistory;</span>
+									<span class="sync-reset-option-desc">&zotero.preferences.sync.reset.resetFileSyncHistory.desc;</span>
+								</label>
+							</li>
+						</ul>
 						
-						<hbox>
-							<button label="&zotero.preferences.sync.reset.button;"
-								oncommand="document.getElementById('sync-reset-rows').firstChild.firstChild.click(); Zotero_Preferences.Sync.handleSyncReset('full-sync')"/>
-						</hbox>
-					</groupbox>
-					
-					<groupbox>
-						<caption label="&zotero.preferences.sync.fileSyncing;"/>
-						
-						<radiogroup oncommand="Zotero_Preferences.Sync.handleSyncResetSelect(this)">
-							<grid>
-								<columns>
-									<column/>
-									<column align="start" pack="start" flex="1"/>
-								</columns>
-								
-								<rows id="storage-reset-rows">
-									<row id="zotero-reset-storage-history">
-										<radio hidden="true"/>
-										<vbox onclick="this.previousSibling.click()">
-											<label value="&zotero.preferences.sync.reset.resetFileSyncHistory;"/>
-											<description>&zotero.preferences.sync.reset.resetFileSyncHistory.desc;</description>
-										</vbox>
-									</row>
-								</rows>
-							</grid>
-						</radiogroup>
-						
-						<hbox>
-							<button label="&zotero.preferences.sync.reset.button;"
-								oncommand="document.getElementById('storage-reset-rows').firstChild.firstChild.click(); Zotero_Preferences.Sync.handleSyncReset('reset-storage-history')"/>
-						</hbox>
-					</groupbox>
+						<button id="sync-reset-button"
+							disabled="disabled"
+							onclick="Zotero_Preferences.Sync.reset()">&zotero.preferences.sync.reset.button;</button>
+					</div>
 				</tabpanel>
 			</tabpanels>
 		</tabbox>

chrome/content/zotero/progressMeterWindow.xul

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+
+<?xml-stylesheet href="chrome://global/skin/" type="text/css"?>
+<?xml-stylesheet href="chrome://zotero/skin/zotero.css" type="text/css"?>
+
+<window id="zotero-progress-meter-window"
+        xmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"
+        windowtype="alert:alert">
+		
+	<vbox id="zotero-progress-text-box" flex="1">
+		<label/>
+		<progressmeter/>
+	</vbox>
+</window>

chrome/content/zotero/recognizePDF.js

@@ -1,943 +0,0 @@
-/*
-    ***** BEGIN LICENSE BLOCK *****
-    
-    Copyright © 2009 Center for History and New Media
-                     George Mason University, Fairfax, Virginia, USA
-                     http://zotero.org
-    
-    This file is part of Zotero.
-    
-    Zotero is free software: you can redistribute it and/or modify
-    it under the terms of the GNU Affero General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-    
-    Zotero is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU Affero General Public License for more details.
-    
-    You should have received a copy of the GNU Affero General Public License
-    along with Zotero.  If not, see <http://www.gnu.org/licenses/>.
-    
-    ***** END LICENSE BLOCK *****
-*/
-
-/**
- * @fileOverview Tools for automatically retrieving a citation for the given PDF
- */
-
-/**
- * Front end for recognizing PDFs
- * @namespace
- */
-var Zotero_RecognizePDF = new function() {
-	var _progressWindow, _progressIndicator;
-	
-	/**
-	 * Checks whether a given PDF could theoretically be recognized
-	 * @returns {Boolean} True if the PDF can be recognized, false if it cannot be
-	 */
-	this.canRecognize = function(/**Zotero.Item*/ item) {
-		return item.attachmentMIMEType
-			&& item.attachmentMIMEType == "application/pdf"
-			&& item.isTopLevelItem();
-	}
-	
-	/**
-	 * Retrieves metadata for the PDF(s) selected in the Zotero Pane, placing the PDFs as a children
-	 * of the new items
-	 */
-	this.recognizeSelected = function() {
-		var installed = ZoteroPane_Local.checkPDFConverter();
-		if (!installed) {
-			return;
-		}
-		
-		var items = ZoteroPane_Local.getSelectedItems();
-		if (!items) return;
-		var itemRecognizer = new Zotero_RecognizePDF.ItemRecognizer();
-		itemRecognizer.recognizeItems(items);
-	}	
-	
-	/**
-	 * Retrieves metadata for a PDF and saves it as an item
-	 *
-	 * @param {nsIFile} file The PDF file to retrieve metadata for
-	 * @param {Integer} libraryID The library in which to save the PDF
-	 * @param {Function} stopCheckCallback Function that returns true if the
-	 *                   process is to be interrupted
-	 * @return {Promise} A promise resolved when PDF metadata has been retrieved
-	 */
-	this.recognize = Zotero.Promise.coroutine(function* (file, libraryID, stopCheckCallback) {
-		const MAX_PAGES = 15;
-		var me = this;
-		
-		var lines = yield _extractText(file, MAX_PAGES);
-		// Look for DOI - Use only first 80 lines to avoid catching article references
-		var allText = lines.join("\n"),
-			firstChunk = lines.slice(0,80).join('\n'),
-			doi = Zotero.Utilities.cleanDOI(firstChunk),
-			promise;
-		Zotero.debug(allText);
-		
-		if(!doi) {
-			// Look for a JSTOR stable URL, which can be converted to a DOI by prepending 10.2307
-			doi = firstChunk.match(/www.\jstor\.org\/stable\/(\S+)/i);
-			if(doi) {
-				doi = Zotero.Utilities.cleanDOI(
-					doi[1].indexOf('10.') == 0 ? doi[1] : '10.2307/' + doi[1]
-				);
-			}
-		}
-		
-		var newItem;
-		if (doi) {
-			// Look up DOI
-			Zotero.debug("RecognizePDF: Found DOI: "+doi);
-			
-			var translateDOI = new Zotero.Translate.Search();
-			translateDOI.setTranslator("11645bd1-0420-45c1-badb-53fb41eeb753");
-			translateDOI.setSearch({"itemType":"journalArticle", "DOI":doi});
-			try {
-				newItem = yield _promiseTranslate(translateDOI, libraryID);
-				return newItem;
-			}
-			catch (e) {
-				Zotero.debug("RecognizePDF: " + e);
-			}
-		}
-		else {
-			Zotero.debug("RecognizePDF: No DOI found in text");
-		}
-		
-		// Look for ISBNs if no DOI
-		var isbns = _findISBNs(allText);
-		if (isbns.length) {
-			Zotero.debug("RecognizePDF: Found ISBNs: " + isbns);
-			
-			var translate = new Zotero.Translate.Search();
-			translate.setSearch({"itemType":"book", "ISBN":isbns[0]});
-			try {
-				newItem = yield _promiseTranslate(translate, libraryID);
-				return newItem;
-			}
-			catch (e) {
-				// If no DOI or ISBN, query Google Scholar
-				Zotero.debug("RecognizePDF: " + e);
-			}
-		}
-		else {
-			Zotero.debug("RecognizePDF: No ISBN found in text");
-		}
-		
-		return this.GSFullTextSearch.findItem(lines, libraryID, stopCheckCallback);
-	});
-	
-	/**
-	 * Get text from a PDF
-	 * @param {nsIFile} file PDF
-	 * @param {Number} pages Number of pages to extract
-	 * @return {Promise}
-	 */
-	function _extractText(file, pages) {
-		var cacheFile = Zotero.File.pathToFile(Zotero.DataDirectory.dir);
-		cacheFile.append("recognizePDFcache.txt");
-		if(cacheFile.exists()) {
-			cacheFile.remove(false);
-		}
-		
-		var {exec, args} = Zotero.Fulltext.getPDFConverterExecAndArgs();
-		args.push('-enc', 'UTF-8', '-nopgbrk', '-layout', '-l', pages, file.path, cacheFile.path);
-		
-		Zotero.debug("RecognizePDF: Running " + exec.path + " " + args.map(arg => "'" + arg + "'").join(" "));
-		
-		return Zotero.Utilities.Internal.exec(exec, args).then(function() {
-			if(!cacheFile.exists()) {
-				throw new Zotero.Exception.Alert("recognizePDF.couldNotRead");
-			}
-			
-			try {
-				var inputStream = Components.classes["@mozilla.org/network/file-input-stream;1"]
-					.createInstance(Components.interfaces.nsIFileInputStream);
-				inputStream.init(cacheFile, 0x01, 0o664, 0);
-				try {
-					var intlStream = Components.classes["@mozilla.org/intl/converter-input-stream;1"]
-						.createInstance(Components.interfaces.nsIConverterInputStream);
-					intlStream.init(inputStream, "UTF-8", 65535,
-						Components.interfaces.nsIConverterInputStream.DEFAULT_REPLACEMENT_CHARACTER);
-					intlStream.QueryInterface(Components.interfaces.nsIUnicharLineInputStream);
-					
-					// get the lines in this sample
-					var lines = [], str = {};
-					while(intlStream.readLine(str)) {
-						var line = str.value.trim();
-						if(line) lines.push(line);
-					}
-				} finally {
-					inputStream.close();
-				}
-			} finally {
-				cacheFile.remove(false);
-			}
-			
-			return lines;
-		}, function() {
-			throw new Zotero.Exception.Alert("recognizePDF.couldNotRead");
-		});
-	}
-	
-	/**
-	 * Attach appropriate handlers to a Zotero.Translate instance and begin translation
-	 * @return {Promise}
-	 */
-	var _promiseTranslate = Zotero.Promise.coroutine(function* (translate, libraryID) {
-		translate.setHandler("select", function(translate, items, callback) {
-			for(var i in items) {
-				var obj = {};
-				obj[i] = items[i];
-				callback(obj);
-				return;
-			}
-		});
-		/*translate.setHandler("done", function(translate, success) {
-			if(success && translate.newItems.length) {
-				deferred.resolve(translate.newItems[0]);
-			} else {
-				deferred.reject(translate.translator && translate.translator.length
-					? "Translation with " + translate.translator.map(t => t.label) + " failed"
-					: "Could not find a translator for given search item"
-				);
-			}
-		});*/
-		var newItems = yield translate.translate({
-			libraryID,
-			saveAttachments: false
-		});
-		if (newItems.length) {
-			return newItems[0];
-		}
-		throw new Error("No items found");
-	});
-	
-	/**
-	 * Search ISBNs in text
-	 * @private
-	 * @return {String[]} Array of ISBNs
-	 */
-	function _findISBNs(x) {
-		if(typeof(x) != "string") {
-			throw "findISBNs: argument must be a string";
-		}
-		var isbns = [];
-	
-		// Match lines saying "isbn: " or "ISBN-10:" or similar, consider m-dashes and n-dashes as well
-		var pattern = /(SBN|sbn)[ \u2014\u2013\u2012-]?(10|13)?[: ]*([0-9X][0-9X \u2014\u2013\u2012-]+)/g; 
-		var match;
-		
-		while (match = pattern.exec(x)) {
-			var isbn = match[3];
-			isbn = isbn.replace(/[ \u2014\u2013\u2012-]/g, '');
-			if(isbn.length==20 || isbn.length==26) { 
-				// Handle the case of two isbns (e.g. paper+hardback) next to each other
-				isbns.push(isbn.slice(0,isbn.length/2), isbn.slice(isbn.length/2));
-			} else if(isbn.length==23) { 
-				// Handle the case of two isbns (10+13) next to each other
-				isbns.push(isbn.slice(0,10), isbn.slice(10));
-			} else if(isbn.length==10 || isbn.length==13) {
-				isbns.push(isbn);
-			}
-		}
-	
-		// Validate ISBNs
-		var validIsbns = [], cleanISBN;
-		for (var i =0; i < isbns.length; i++) {
-			cleanISBN = Zotero.Utilities.cleanISBN(isbns[i]);
-			if(cleanISBN) validIsbns.push(cleanISBN);
-		}
-		return validIsbns;
-	}
-	
-	/**
-	 * @class Handles UI, etc. for recognizing multiple items
-	 */
-	this.ItemRecognizer = function () {
-		this._items = [];
-	}
-
-	this.ItemRecognizer.prototype = {
-		"_stopped": false,
-		"_itemsTotal": 0,
-		"_progressWindow": null,
-		"_progressIndicator": null,
-
-		/**
-		 * Retreives metadata for the PDF items passed, displaying a progress dialog during conversion 
-		 * and placing the PDFs as a children of the new items
-		 * @param {Zotero.Item[]} items
-		 */
-		"recognizeItems": function(items) {
-			var me = this;
-			this._items = items.slice();
-			this._itemTotal = items.length;
-			
-			_progressWindow = this._progressWindow = window.openDialog("chrome://zotero/content/pdfProgress.xul", "", "chrome,close=yes,resizable=yes,dependent,dialog,centerscreen");
-			this._progressWindow.addEventListener("pageshow", function() { me._onWindowLoaded() }, false);
-		},
-
-		/**
-		 * Halts recognition of PDFs
-		 */
-		"stop": function() {
-			this._stopped = true;	
-		},
-		
-		/**
-		 * Halts recognition and closes window
-		 */
-		"close": function() {
-			this.stop();
-			this._progressWindow.close();
-		},
-		
-		/**
-		 * Called when the progress window has been opened; adds items to the tree and begins recognizing
-		 * @param
-		 */
-		"_onWindowLoaded": function() {
-			// populate progress window
-			var treechildren = this._progressWindow.document.getElementById("treechildren");
-			this._rowIDs = [];
-			for(var i in this._items) {
-				var treeitem = this._progressWindow.document.createElement('treeitem');
-				var treerow = this._progressWindow.document.createElement('treerow');
-				this._rowIDs.push(this._items[i].id);
-				
-				var treecell = this._progressWindow.document.createElement('treecell');
-				treecell.setAttribute("id", "item-"+this._items[i].id+"-icon");
-				treerow.appendChild(treecell);
-				
-				treecell = this._progressWindow.document.createElement('treecell');
-				treecell.setAttribute("label", this._items[i].getField("title"));
-				treerow.appendChild(treecell);
-				
-				treecell = this._progressWindow.document.createElement('treecell');
-				treecell.setAttribute("id", "item-"+this._items[i].id+"-title");
-				treerow.appendChild(treecell);
-				
-				treeitem.appendChild(treerow);
-				treechildren.appendChild(treeitem);
-			}
-			
-			var me = this;
-			
-			this._progressWindow.document.getElementById("tree").addEventListener(
-				"dblclick", function(event) { me._onDblClick(event, this); });
-			
-			this._cancelHandler = function() { me.stop() };
-			this._keypressCancelHandler = function(e) {
-				if(e.keyCode === KeyEvent.DOM_VK_ESCAPE) me.stop();
-			};
-			
-			_progressIndicator = this._progressIndicator = this._progressWindow.document.getElementById("progress-indicator");
-			this._progressWindow.document.getElementById("cancel-button")
-				.addEventListener("command", this._cancelHandler, false);
-			// Also cancel if the user presses Esc
-			this._progressWindow.addEventListener("keypress", this._keypressCancelHandler);
-			this._progressWindow.addEventListener("close", this._cancelHandler, false);
-			Zotero_RecognizePDF.GSFullTextSearch.resetQueryLimit();
-			return this._recognizeItem();
-		},
-
-		/**
-		 * Shifts an item off of this._items and recognizes it, then calls itself again if there are more
-		 * @private
-		 */
-		"_recognizeItem": Zotero.Promise.coroutine(function* () {
-			const SUCCESS_IMAGE = "chrome://zotero/skin/tick.png";
-			const FAILURE_IMAGE = "chrome://zotero/skin/cross.png";
-			const LOADING_IMAGE = "chrome://global/skin/icons/loading_16.png";
-
-			if(!this._items.length) {
-				this._done();
-				return;
-			}
-			
-			// Order here matters. Otherwise we may show an incorrect label
-			if(this._stopped) {
-				this._done(true);
-				return;
-			}
-			
-			this._progressIndicator.value = (this._itemTotal-this._items.length)/this._itemTotal*100;
-			
-			var item = this._items.shift(),
-				itemIcon = this._progressWindow.document.getElementById("item-"+item.id+"-icon"),
-				itemTitle = this._progressWindow.document.getElementById("item-"+item.id+"-title"),
-				rowNumber = this._rowIDs.indexOf(item.id);
-			itemIcon.setAttribute("src", LOADING_IMAGE);
-			itemTitle.setAttribute("label", "");
-			
-			var file = item.getFile(), me = this;
-			
-			try {
-				if (file) {
-					let newItem = yield Zotero_RecognizePDF.recognize(
-						file,
-						item.libraryID,
-						() => this._stopped
-					);
-					
-					// If already stopped, delete
-					if (this._stopped) {
-						yield Zotero.Items.erase(newItem.id);
-						throw new Zotero.Exception.Alert('recognizePDF.stopped');
-					}
-					
-					// put new item in same collections as the old one
-					let itemCollections = item.getCollections();
-					yield Zotero.DB.executeTransaction(function* () {
-						for (let i = 0; i < itemCollections.length; i++) {
-							let collection = Zotero.Collections.get(itemCollections[i]);
-							yield collection.addItem(newItem.id);
-						}
-
-						// put old item as a child of the new item
-						item.parentID = newItem.id;
-						yield item.save();
-					});
-					
-					itemTitle.setAttribute("label", newItem.getField("title"));
-					itemIcon.setAttribute("src", SUCCESS_IMAGE);
-					this._rowIDs[rowNumber] = newItem.id;
-					
-					return this._recognizeItem();
-				}
-				else {
-					throw new Zotero.Exception.Alert("recognizePDF.fileNotFound");
-				}
-			}
-			catch (e) {
-				Zotero.logError(e);
-
-				itemTitle.setAttribute(
-					"label",
-					e instanceof Zotero.Exception.Alert
-						? e.message
-						: Zotero.getString("recognizePDF.error")
-				);
-				itemIcon.setAttribute("src", FAILURE_IMAGE);
-				
-				// Don't show "completed" label if stopped on last item
-				if (this._stopped && !this._items.length) {
-					this._done(true);
-				} else {
-					return this._recognizeItem();
-				}
-			}
-			finally {
-				// scroll to this item
-				this._progressWindow.document.getElementById("tree").treeBoxObject.scrollToRow(
-					Math.max(0, this._itemTotal - this._items.length - 4)
-				);
-			}
-		}),
-
-		/**
-		 * Cleans up after items are recognized, disabling the cancel button and
-		 * making the progress window close on blur.
-		 * @param {Boolean} cancelled Whether the process was cancelled
-		 */
-		"_done": function(cancelled) {
-			this._progressIndicator.value = 100;
-			// Switch out cancel for close
-			var cancelButton = this._progressWindow.document.getElementById("cancel-button"),
-				me = this;
-			cancelButton.label = Zotero.getString("recognizePDF.close.label");
-			cancelButton.removeEventListener("command", this._cancelHandler, false);
-			cancelButton.addEventListener("command", function() { me.close() }, false);
-			this._progressWindow.removeEventListener("keypress", this._keypressCancelHandler);
-			this._progressWindow.addEventListener("keypress", function() { me.close() });
-			
-			if(Zotero.isMac) {
-				// On MacOS X, the windows are not always on top, so we hide them on
-				// blur to avoid clutter
-				this._setCloseTimer();
-			}
-			this._progressWindow.document.getElementById("label").value = 
-				cancelled ? Zotero.getString("recognizePDF.cancelled.label")
-					: Zotero.getString("recognizePDF.complete.label");
-		},
-		
-		/**
-		 * Set a timer after which the window will close automatically. If the
-		 * window is refocused, clear the timer and do not attempt to auto-close
-		 * any more
-		 * @private
-		 */
-		"_setCloseTimer": function() {
-			var me = this, win = this._progressWindow;
-			var focusListener = function() {
-				if(!win.zoteroCloseTimeoutID) return;
-				
-				win.clearTimeout(win.zoteroCloseTimeoutID);
-				delete win.zoteroCloseTimeoutID;
-				
-				win.removeEventListener('blur', blurListener, false);
-				win.removeEventListener('focus', focusListener, false);
-			};
-			var blurListener = function() {
-				// Close window after losing focus for 5 seconds
-				win.zoteroCloseTimeoutID = win.setTimeout(function() { win.close() }, 5000);
-				// Prevent auto-close if we gain focus again
-				win.addEventListener("focus", focusListener, false);
-			};
-			win.addEventListener("blur", blurListener, false);
-		},
-		
-		/**
-		 * Focus items in Zotero library when double-clicking them in the Retrieve
-		 * metadata window.
-		 * @param {Event} event
-		 * @param {tree} tree XUL tree object
-		 * @private
-		 */
-		"_onDblClick": function(event, tree) {
-			if (event && tree && event.type == "dblclick") {
-				var itemID = this._rowIDs[tree.treeBoxObject.getRowAt(event.clientX, event.clientY)];
-				if(!itemID) return;
-				
-				// Get the right window. In tab mode, it's the container window
-				var lastWin = (window.ZoteroTab ? window.ZoteroTab.containerWindow : window);
-				
-				if (lastWin.ZoteroOverlay) {
-					lastWin.ZoteroOverlay.toggleDisplay(true);
-				}
-				
-				lastWin.ZoteroPane.selectItem(itemID, false, true);
-				lastWin.focus();
-			}
-		}
-	};
-	
-	/**
-	 * Singleton for querying Google Scholar. Ensures that all queries are
-	 * sequential and respect the delay inbetween queries.
-	 * @namespace
-	 */
-	this.GSFullTextSearch = new function() {
-		const GOOGLE_SCHOLAR_QUERY_DELAY = 2000; // In ms
-		var queryLimitReached = false,
-			inProgress = false,
-			queue = [],
-			stopCheckCallback; // As long as we process one query at a time, this is ok
-		// Load nsICookieManager2
-		Components.utils.import("resource://gre/modules/Services.jsm");
-		var cookieService = Services.cookies;
-		
-		/**
-		 * Reset "Query Limit Reached" flag, so that we attempt to query Google again
-		 */
-		this.resetQueryLimit = function() {
-			queryLimitReached = false;
-		};
-		
-		/**
-		 * Queue up item for Google Scholar query
-		 * @param {String[]} lines Lines of text to use for full-text query
-		 * @param {Integer | null} libraryID Library to save the item to
-		 * @param {Function} stopCheckCallback Function that returns true if the
-		 *                   process is to be interrupted
-		 * @return {Promise} A promise resolved when PDF metadata has been retrieved
-		 */
-		this.findItem = function(lines, libraryID, stopCheckCallback) {
-			if(!inProgress && queryLimitReached) {
-				// There's no queue, so we can reject immediately
-				return Zotero.Promise.reject(new Zotero.Exception.Alert("recognizePDF.limit"));
-			}
-			
-			var deferred = Zotero.Promise.defer();
-			queue.push({
-				deferred: deferred,
-				lines: lines,
-				libraryID: libraryID,
-				stopCheckCallback: stopCheckCallback
-			});
-			_processQueue();
-			return deferred.promise;
-		};
-		
-		/**
-		 * Process Google Scholar queue
-		 * @private
-		 * @param {Boolean} proceed Whether we should pop the next item off the queue
-		 *                  This should not be true unless being called after processing
-		 *                  another item
-		 */
-		function _processQueue(proceed) {
-			if(inProgress && !proceed) return; //only one at a time
-			
-			if(!queue.length) {
-				inProgress = false;
-				return;
-			}
-			
-			inProgress = true;
-			if(queryLimitReached) {
-				// Irreversibly blocked. Reject remaining items in queue
-				var item;
-				while(item = queue.shift()) {
-					item.deferred.reject(new Zotero.Exception.Alert("recognizePDF.limit"));
-				}
-				_processQueue(true); // Wrap it up
-			} else {
-				var item = queue.shift();
-				
-				stopCheckCallback = item.stopCheckCallback;
-				if(stopCheckCallback && stopCheckCallback()) {
-					item.deferred.reject(new Zotero.Exception.Alert('recognizePDF.stopped'));
-					_processQueue(true);
-					return;
-				}
-				
-				item.deferred.resolve(
-					Zotero.Promise.try(function () {
-						var lines = getGoodLines(item.lines);
-						return queryGoogle(lines, item.libraryID, 3); // Try querying 3 times
-					})
-					.finally(function() { _processQueue(true); })
-				);
-			}
-		}
-		
-		/**
-		 * Select lines that are good candidates for Google Scholar query
-		 * @private
-		 * @param {String[]} lines
-		 * @return {String[]}
-		 */
-		function getGoodLines(lines) {
-			// Use only first column from multi-column lines
-			const lineRe = /^[\s_]*([^\s]+(?: [^\s_]+)+)/;
-			var cleanedLines = [], cleanedLineLengths = [];
-			for(var i=0; i<lines.length && cleanedLines.length<100; i++) {
-				var m = lineRe.exec(
-					lines[i]
-					// Replace non-breaking spaces
-					.replace(/\xA0/g, ' ')
-				);
-				if(m && m[1].split(' ').length > 3) {
-					cleanedLines.push(m[1]);
-					cleanedLineLengths.push(m[1].length);
-				}
-			}
-			
-			// Get (not quite) median length
-			var lineLengthsLength = cleanedLineLengths.length;
-			if(lineLengthsLength < 20
-					|| cleanedLines[0] === "This is a digital copy of a book that was preserved for generations on library shelves before it was carefully scanned by Google as part of a project") {
-				throw new Zotero.Exception.Alert("recognizePDF.noOCR");
-			}
-			
-			var sortedLengths = cleanedLineLengths.sort(),
-				medianLength = sortedLengths[Math.floor(lineLengthsLength/2)];
-			
-			// Pick lines within 6 chars of the median (this is completely arbitrary)
-			var goodLines = [],
-				uBound = medianLength + 6,
-				lBound = medianLength - 6;
-			for (var i=0; i<lineLengthsLength; i++) {
-				if(cleanedLineLengths[i] > lBound && cleanedLineLengths[i] < uBound) {
-					// Strip quotation marks so they don't mess up search query quoting
-					var line = cleanedLines[i].replace('"', '');
-					goodLines.push(line);
-				}
-			}
-			return goodLines;
-		}
-		
-		/**
-		 * Query Google Scholar
-		 * @private
-		 * @param {String[]} goodLines
-		 * @param {Integer | null} libraryID
-		 * @param {Integer} tries Number of queries to attempt before giving up
-		 * @return {Promise} A promise resolved when PDF metadata has been retrieved
-		 */
-		var queryGoogle = Zotero.Promise.coroutine(function* (goodLines, libraryID, tries) {
-			if(tries <= 0) throw new Zotero.Exception.Alert("recognizePDF.noMatches");
-			
-			// Take the relevant parts of some lines (exclude hyphenated word)
-			var queryString = "", queryStringWords = 0, nextLine = 0;
-			while(queryStringWords < 25) {
-				if(!goodLines.length) throw new Zotero.Exception.Alert("recognizePDF.noMatches");
-		
-				var words = goodLines.splice(nextLine, 1)[0].split(/\s+/);
-				// Try to avoid picking adjacent strings so the odds of them appearing in another
-				// document quoting our document is low. Every 7th line is a magic value
-				nextLine = (nextLine + 7) % goodLines.length;
-		
-				// Get rid of first and last words
-				words.shift();
-				words.pop();
-				// Make sure there are no long words (probably OCR mistakes)
-				var skipLine = false;
-				for(var i=0; i<words.length; i++) {
-					if(words[i].length > 20) {
-						skipLine = true;
-						break;
-					}
-				}
-				// Add words to query
-				if(!skipLine && words.length) {
-					queryStringWords += words.length;
-					queryString += '"'+words.join(" ")+'" ';
-				}
-			}
-			
-			Zotero.debug("RecognizePDF: Query string " + queryString);
-			
-			var url = "https://scholar.google.com/scholar?q="+encodeURIComponent(queryString)+"&hl=en&lr=&btnG=Search",
-				delay = GOOGLE_SCHOLAR_QUERY_DELAY - (Date.now() - Zotero.HTTP.lastGoogleScholarQueryTime);
-
-			// Delay 
-			if (delay > 0) {
-				yield Zotero.Promise.delay(delay);
-			}
-			Zotero.HTTP.lastGoogleScholarQueryTime = Date.now();
-			try {
-				let xmlhttp = yield Zotero.HTTP.request("GET", url, { "responseType": "document" })
-					.then(
-						function (xmlhttp) {
-							return _checkCaptchaOK(xmlhttp, 3);
-						},
-						function (e) {
-							return _checkCaptchaError(e, 3);
-						}
-					);
-				
-				let doc = xmlhttp.response,
-					deferred = Zotero.Promise.defer(),
-					translate = new Zotero.Translate.Web();
-				
-				translate.setTranslator("57a00950-f0d1-4b41-b6ba-44ff0fc30289");
-				translate.setDocument(Zotero.HTTP.wrapDocument(doc, url));
-				translate.setHandler("translators", function(translate, detected) {
-					if(detected.length) {
-						deferred.resolve(_promiseTranslate(translate, libraryID));
-					} else {
-						deferred.resolve(Zotero.Promise.try(function() {
-							return queryGoogle(goodLines, libraryID, tries-1);
-						}));
-					}
-				});
-				translate.getTranslators();
-				
-				return deferred.promise;
-			}
-			catch (e) {
-				if(e.name == "recognizePDF.limit") {
-					queryLimitReached = true;
-				}
-				throw e;
-			}
-		});
-		
-		/**
-		 * Check for CAPTCHA on a page with HTTP 200 status
-		 * @private
-		 * @param {XMLHttpRequest} xmlhttp
-		 * @param {Integer} tries Number of queries to attempt before giving up
-		 * @return {Promise} A promise resolved when PDF metadata has been retrieved
-		 */
-		function _checkCaptchaOK(xmlhttp, tries) {
-			if(stopCheckCallback && stopCheckCallback()) {
-				throw new Zotero.Exception.Alert('recognizePDF.stopped');
-			}
-			
-			Zotero.debug("RecognizePDF: (" + xmlhttp.status + ") Got page with title " + xmlhttp.response.title);
-			
-			if(Zotero.Utilities.xpath(xmlhttp.response, "//form[@action='Captcha']").length) {
-				Zotero.debug("RecognizePDF: Found CAPTCHA on page.");
-				return _solveCaptcha(xmlhttp, tries);
-			}
-			return xmlhttp;
-		}
-		
-		/**
-		 * Check for CAPTCHA on an error page. Handle 403 and 503 pages
-		 * @private
-		 * @param {Zotero.HTTP.UnexpectedStatusException} e HTTP response error object
-		 * @param {Integer} tries Number of queries to attempt before giving up
-		 * @param {Boolean} dontClearCookies Whether to attempt to clear cookies in
-		 *                  in order to get CAPTCHA to show up
-		 * @return {Promise} A promise resolved when PDF metadata has been retrieved
-		 */
-		var _checkCaptchaError = Zotero.Promise.coroutine(function* (e, tries, dontClearCookies) {
-			if(stopCheckCallback && stopCheckCallback()) {
-				throw new Zotero.Exception.Alert('recognizePDF.stopped');
-			}
-			
-			Zotero.debug("RecognizePDF: Checking for CAPTCHA on Google Scholar error page (" + e.status + ")");
-			
-			// Check for captcha on error page
-			if(e instanceof Zotero.HTTP.UnexpectedStatusException
-				&& (e.status == 403 || e.status == 503) && e.xmlhttp.response) {
-				if(_extractCaptchaFormData(e.xmlhttp.response)) {
-					Zotero.debug("RecognizePDF: CAPTCHA found");
-					return _solveCaptcha(e.xmlhttp, tries);
-				} else if(!dontClearCookies && e.xmlhttp.channel) { // Make sure we can obtain original URL
-					// AFAICT, for 403 errors, GS just says "sorry, try later",
-					// but if you clear cookies, you get a CAPTCHA
-					Zotero.debug("RecognizePDF: No CAPTCHA detected on page. Clearing cookies.");
-					if(!_clearGSCookies(e.xmlhttp.channel.originalURI.host)) {
-						//user said no or no cookies removed
-						throw new Zotero.Exception.Alert('recognizePDF.limit');
-					}
-					// Redo GET request
-					Zotero.debug("RecognizePDF: Reloading page after clearing cookies.");
-					return Zotero.HTTP.request(
-						"GET", e.xmlhttp.channel.originalURI.spec, { "responseType": "document" }
-					)
-					.then(
-						function (xmlhttp) {
-							return _checkCaptchaOK(xmlhttp, tries);
-						},
-						function (e) {
-							return _checkCaptchaError(e, tries, true); // Don't try this again
-						}
-					);
-				}
-				
-				Zotero.debug("RecognizePDF: Google Scholar returned an unexpected page"
-					+ " with status " + e.status);
-				throw new Zotero.Exception.Alert('recognizePDF.limit');
-			}
-			throw e;
-		});
-		
-		/**
-		 * Prompt user to enter CPATCHA
-		 * @private
-		 * @param {XMLHttpRequest} xmlhttp
-		 * @param {Integer} [tries] Number of queries to attempt before giving up
-		 * @return {Promise} A promise resolved when PDF metadata has been retrieved
-		 */
-		function _solveCaptcha(xmlhttp, tries) {
-			var doc = xmlhttp.response;
-			
-			if(tries === undefined) tries = 3;
-			
-			if(!tries) {
-				Zotero.debug("RecognizePDF: Failed to solve CAPTCHA after multiple attempts.");
-				throw new Zotero.Exception.Alert('recognizePDF.limit');
-			}
-			
-			tries--;
-			var formData = doc && _extractCaptchaFormData(doc);
-			if(!formData) {
-				Zotero.debug("RecognizePDF: Could not find CAPTCHA on page.");
-				throw new Zotero.Exception.Alert('recognizePDF.limit');
-			}
-	
-			var io = { dataIn: {
-				title: Zotero.getString("recognizePDF.captcha.title"),
-				description: Zotero.getString("recognizePDF.captcha.description"),
-				imgUrl: formData.img
-			}};
-			
-			_progressWindow.openDialog("chrome://zotero/content/captcha.xul", "",
-				"chrome,modal,resizable=no,centerscreen", io);
-			
-			if(!io.dataOut) {
-				Zotero.debug("RecognizePDF: No CAPTCHA entered");
-				throw new Zotero.Exception.Alert('recognizePDF.limit');
-			}
-			
-			Zotero.debug('RecognizePDF: User entered "' + io.dataOut.captcha + '" for CAPTCHA');
-			formData.input.captcha = io.dataOut.captcha;
-			var url = '', prop;
-			for(prop in formData.input) {
-				url += '&' + encodeURIComponent(prop) + '='
-					+ encodeURIComponent(formData.input[prop]);
-			}
-			
-			url = formData.action + '?' + url.substr(1);
-			
-			return Zotero.HTTP.promise("GET", url, {"responseType":"document"})
-				.then(function(xmlhttp) {
-					return _checkCaptchaOK(xmlhttp, tries);
-				},
-				function(e) {
-					return _checkCaptchaError(e, tries);
-				});
-		}
-		
-		/**
-		 * Extract CAPTCHA form-related data from the CAPTCHA page
-		 * @private
-		 * @param {Document} doc DOM document object for the CAPTCHA page
-		 * @return {Object} Object containing data describing CAPTCHA form
-		 */
-		function _extractCaptchaFormData(doc) {
-			var formData = {};
-			
-			var img = doc.getElementsByTagName('img')[0];
-			if(!img) return;
-			formData.img = img.src;
-			
-			var form = doc.forms[0];
-			if(!form) return;
-			
-			formData.action = form.action;
-			formData.input = {};
-			var inputs = form.getElementsByTagName('input');
-			for(var i=0, n=inputs.length; i<n; i++) {
-				if(!inputs[i].name) continue;
-				formData.input[inputs[i].name] = inputs[i].value;
-			}
-			
-			formData.continue = "https://scholar.google.com";
-			
-			return formData;
-		}
-		
-		/**
-		 * Clear Google cookies to get the CAPTCHA page to appear
-		 * @private
-		 * @param {String} host Host of the Google Scholar page (in case it's proxied)
-		 * @return {Boolean} Whether any cookies were cleared
-		 */
-		function _clearGSCookies(host) {
-			/* There don't seem to be any negative effects of deleting GDSESS
-			if(!Zotero.isStandalone) {
-				//ask user first
-				var response = Components.classes["@mozilla.org/embedcomp/prompt-service;1"]
-					.getService(Components.interfaces.nsIPromptService)
-					.confirm(null, "Clear Google Scholar cookies?",
-						"Google Scholar is attempting to block further queries. We can "
-						+ "clear certain cookies and try again. This may affect some "
-						+ "temporary Google preferences or it may log you out. May we clear"
-						+ " your Google Scholar cookies?");
-				if(!response) return;
-			}*/
-			
-			var removed = false, cookies = cookieService.getCookiesFromHost(host);
-			while(cookies.hasMoreElements()) {
-				var cookie = cookies.getNext().QueryInterface(Components.interfaces.nsICookie2);
-				if(["GDSESS", "PREF"].indexOf(cookie.name) !== -1) { // GDSESS doesn't seem to always be enough
-					Zotero.debug("RecognizePDF: Removing cookie " + cookie.name + " for host "
-						+ cookie.host + " and path " + cookie.path);
-					cookieService.remove(cookie.host, cookie.name, cookie.path, false);
-					removed = true;
-				}
-			}
-			
-			if(!removed) {
-				Zotero.debug("RecognizePDF: No cookies removed");
-			}
-			
-			return removed;
-		}
-	};
-}

chrome/content/zotero/recognizePDFDialog.js

@@ -0,0 +1,219 @@
+/*
+    ***** BEGIN LICENSE BLOCK *****
+    
+    Copyright © 2018 Center for History and New Media
+                     George Mason University, Fairfax, Virginia, USA
+                     http://zotero.org
+    
+    This file is part of Zotero.
+    
+    Zotero is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Zotero is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+    
+    You should have received a copy of the GNU Affero General Public License
+    along with Zotero.  If not, see <http://www.gnu.org/licenses/>.
+    
+    ***** END LICENSE BLOCK *****
+*/
+
+/**
+ * @fileOverview Tools for automatically retrieving a citation for the given PDF
+ */
+
+/**
+ * Front end for recognizing PDFs
+ * @namespace
+ */
+
+var Zotero_RecognizePDF_Dialog = new function () {
+	const SUCCESS_IMAGE = 'chrome://zotero/skin/tick.png';
+	const FAILURE_IMAGE = 'chrome://zotero/skin/cross.png';
+	const LOADING_IMAGE = 'chrome://zotero/skin/arrow_refresh.png';
+	
+	let _progressWindow = null;
+	let _progressIndicator = null;
+	let _rowIDs = [];
+	
+	this.open = function() {
+		if (_progressWindow) {
+			_progressWindow.focus();
+			return;
+		}
+		_progressWindow = window.openDialog('chrome://zotero/content/recognizePDFDialog.xul', '', 'chrome,close=yes,resizable=yes,dependent,dialog,centerscreen');
+		_progressWindow.addEventListener('pageshow', _onWindowLoaded.bind(this), false);
+	};
+	
+	function close() {
+		_progressWindow.close();
+	}
+	
+	function _getImageByStatus(status) {
+		if (status === Zotero.RecognizePDF.ROW_PROCESSING) {
+			return LOADING_IMAGE;
+		}
+		else if (status === Zotero.RecognizePDF.ROW_FAILED) {
+			return FAILURE_IMAGE;
+		}
+		else if (status === Zotero.RecognizePDF.ROW_SUCCEEDED) {
+			return SUCCESS_IMAGE;
+		}
+		return '';
+	}
+	
+	function _rowToTreeItem(row) {
+		let treeitem = _progressWindow.document.createElement('treeitem');
+		treeitem.setAttribute('id', 'item-' + row.id);
+		
+		let treerow = _progressWindow.document.createElement('treerow');
+		
+		let treecell = _progressWindow.document.createElement('treecell');
+		treecell.setAttribute('id', 'item-' + row.id + '-icon');
+		treecell.setAttribute('src', _getImageByStatus(row.status));
+		
+		treerow.appendChild(treecell);
+		
+		treecell = _progressWindow.document.createElement('treecell');
+		treecell.setAttribute('label', row.fileName);
+		treerow.appendChild(treecell);
+		
+		treecell = _progressWindow.document.createElement('treecell');
+		treecell.setAttribute('id', 'item-' + row.id + '-title');
+		treecell.setAttribute('label', row.message);
+		treerow.appendChild(treecell);
+		
+		treeitem.appendChild(treerow);
+		return treeitem;
+	}
+	
+	function _onWindowLoaded() {
+		let rows = Zotero.RecognizePDF.getRows();
+		_rowIDs = [];
+		let treechildren = _progressWindow.document.getElementById('treechildren');
+		
+		for (let row of rows) {
+			_rowIDs.push(row.id);
+			let treeitem = _rowToTreeItem(row);
+			treechildren.appendChild(treeitem);
+		}
+		
+		_progressWindow.document.getElementById('tree').addEventListener('dblclick',
+			function (event) {
+				_onDblClick(event, this);
+			}
+		);
+		
+		_progressIndicator = _progressWindow.document.getElementById('progress-indicator');
+		_progressWindow.document.getElementById('cancel-button')
+			.addEventListener('command', function () {
+				close();
+				Zotero.RecognizePDF.cancel();
+			}, false);
+		
+		_progressWindow.document.getElementById('minimize-button')
+			.addEventListener('command', function () {
+				close();
+			}, false);
+		
+		_progressWindow.document.getElementById('close-button')
+			.addEventListener('command', function () {
+				close();
+				Zotero.RecognizePDF.cancel();
+			}, false);
+		
+		_progressWindow.addEventListener('keypress', function (e) {
+			if (e.keyCode === KeyEvent.DOM_VK_ESCAPE) {
+				// If done processing, Esc is equivalent to Close rather than Minimize
+				if (Zotero.RecognizePDF.getTotal() == Zotero.RecognizePDF.getProcessedTotal()) {
+					Zotero.RecognizePDF.cancel();
+				}
+				close();
+			}
+		});
+		
+		_progressWindow.addEventListener('unload', function () {
+			Zotero.RecognizePDF.removeListener('rowadded');
+			Zotero.RecognizePDF.removeListener('rowupdated');
+			Zotero.RecognizePDF.removeListener('rowdeleted');
+			_progressWindow = null;
+			_progressIndicator = null;
+			_rowIDs = [];
+		});
+		
+		_updateProgress();
+		
+		Zotero.RecognizePDF.addListener('rowadded', function (row) {
+			_rowIDs.push(row.id);
+			let treeitem = _rowToTreeItem(row);
+			treechildren.appendChild(treeitem);
+			_updateProgress();
+		});
+		
+		Zotero.RecognizePDF.addListener('rowupdated', function (row) {
+			let itemIcon = _progressWindow.document.getElementById('item-' + row.id + '-icon');
+			let itemTitle = _progressWindow.document.getElementById('item-' + row.id + '-title');
+			
+			itemIcon.setAttribute('src', _getImageByStatus(row.status));
+			itemTitle.setAttribute('label', row.message);
+			_updateProgress();
+		});
+		
+		Zotero.RecognizePDF.addListener('rowdeleted', function (row) {
+			_rowIDs.splice(_rowIDs.indexOf(row.id), 1);
+			let treeitem = _progressWindow.document.getElementById('item-' + row.id);
+			treeitem.parentNode.removeChild(treeitem);
+			_updateProgress();
+		});
+	}
+	
+	function _updateProgress() {
+		if (!_progressWindow) return;
+		let total = Zotero.RecognizePDF.getTotal();
+		let processed = Zotero.RecognizePDF.getProcessedTotal();
+		_progressIndicator.value = processed * 100 / total;
+		if (processed === total) {
+			_progressWindow.document.getElementById("cancel-button").hidden = true;
+			_progressWindow.document.getElementById("minimize-button").hidden = true;
+			_progressWindow.document.getElementById("close-button").hidden = false;
+			_progressWindow.document.getElementById("label").value = Zotero.getString('recognizePDF.complete.label');
+		}
+		else {
+			_progressWindow.document.getElementById("cancel-button").hidden = false;
+			_progressWindow.document.getElementById("minimize-button").hidden = false;
+			_progressWindow.document.getElementById("close-button").hidden = true;
+			_progressWindow.document.getElementById("label").value = Zotero.getString('recognizePDF.recognizing.label');
+		}
+	}
+	
+	/**
+	 * Focus items in Zotero library when double-clicking them in the Retrieve
+	 * metadata window.
+	 * @param {Event} event
+	 * @param {tree} tree XUL tree object
+	 * @private
+	 */
+	async function _onDblClick(event, tree) {
+		if (event && tree && event.type === 'dblclick') {
+			let itemID = _rowIDs[tree.treeBoxObject.getRowAt(event.clientX, event.clientY)];
+			if (!itemID) return;
+			
+			let item = await Zotero.Items.getAsync(itemID);
+			if (!item) return;
+			
+			if (item.parentItemID) itemID = item.parentItemID;
+			
+			if (window.ZoteroOverlay) {
+				window.ZoteroOverlay.toggleDisplay(true);
+			}
+			
+			window.ZoteroPane.selectItem(itemID, false, true);
+			window.focus();
+		}
+	}
+};

chrome/content/zotero/recognizePDFDialog.xul

@@ -6,10 +6,12 @@
 	title="&zotero.progress.title;" width="550" height="230"
 	id="zotero-progress">
 	<vbox style="padding:10px" flex="1">
-		<label id="label" control="progress-indicator" value="&zotero.recognizePDF.recognizing.label;"/>
+		<label id="label" control="progress-indicator" value=""/>
 		<hbox align="center">
 			<progressmeter id="progress-indicator" mode="determined" flex="1"/>
-			<button id="cancel-button" label="&zotero.recognizePDF.cancel.label;"/>
+			<button id="cancel-button" label="&zotero.general.cancel;"/>
+			<button id="minimize-button" label="&zotero.general.minimize;"/>
+			<button id="close-button" label="&zotero.general.close;"/>
 		</hbox>
 		<tree flex="1" id="tree" hidecolumnpicker="true">
 			<treecols>

chrome/content/zotero/standalone/standalone.js

@@ -139,6 +139,15 @@ const ZoteroStandalone = new function() {
 	
 	
 	this.updateQuickCopyOptions = function () {
+		var selected = false;
+		try {
+			selected = Zotero.getActiveZoteroPane()
+				.getSelectedItems()
+				.filter(item => item.isRegularItem())
+				.length;
+		}
+		catch (e) {}
+		
 		var format = Zotero.QuickCopy.getFormatFromURL(Zotero.QuickCopy.lastActiveURL);
 		format = Zotero.QuickCopy.unserializeSetting(format);
 		
@@ -146,16 +155,18 @@ const ZoteroStandalone = new function() {
 		var copyBibliography = document.getElementById('menu_copyBibliography');
 		var copyExport = document.getElementById('menu_copyExport');
 		
-		copyCitation.hidden = format.mode != 'bibliography';
-		copyBibliography.hidden = format.mode != 'bibliography';
-		copyExport.hidden = format.mode != 'export';
+		copyCitation.hidden = !selected || format.mode != 'bibliography';
+		copyBibliography.hidden = !selected || format.mode != 'bibliography';
+		copyExport.hidden = !selected || format.mode != 'export';
 		if (format.mode == 'export') {
 			try {
 				let obj = Zotero.Translators.get(format.id);
 				copyExport.label = Zotero.getString('quickCopy.copyAs', obj.label);
 			}
 			catch (e) {
-				Zotero.logError(e);
+				if (!(e instanceof Zotero.Exception.UnloadedDataException && e.dataType == 'translators')) {
+					Zotero.logError(e);
+				}
 				copyExport.hidden = true;
 			}
 		}
@@ -270,6 +281,8 @@ ZoteroStandalone.DebugOutput = {
 	submit: function () {
 		// 'Zotero' isn't defined yet when this function is created, so do it inline
 		return Zotero.Promise.coroutine(function* () {
+			Zotero.debug("Submitting debug output");
+			
 			Components.utils.import("resource://zotero/config.js");
 			
 			var url = ZOTERO_CONFIG.REPOSITORY_URL + "report?debug=1";

chrome/content/zotero/standalone/standalone.xul

@@ -60,7 +60,7 @@
 		<!--EDIT-->
 		<commandset id="editMenuCommands"/>
 		<command id="cmd_find"
-			oncommand="document.getElementById('zotero-tb-search').focus();"/>
+			oncommand="document.getElementById('zotero-tb-search').select()"/>
 	</commandset>
 	
 	<keyset id="mainKeyset">

chrome/content/zotero/tagColorChooser.js

@@ -52,9 +52,9 @@ var Zotero_Tag_Color_Chooser = new function() {
 			colorPicker.setAttribute('tileWidth', 24);
 			colorPicker.setAttribute('tileHeight', 24);
 			colorPicker.colors = [
-				'#990000', '#CC9933', '#FF9900',
-				'#FFCC00', '#007439', '#1049A9',
-				'#9999FF', '#CC66CC', '#993399'
+				'#FF6666', '#FF8C19', '#999999',
+				'#5FB236', '#009980', '#2EA8E5',
+				'#576DD9', '#A28AE5', '#A6507B'
 			];
 			
 			var maxTags = document.getElementById('max-tags');

chrome/content/zotero/tools/build_typeSchemaData.html

@@ -30,7 +30,7 @@
 		for (let type of types) {
 			var fieldIDs = Zotero.ItemFields.getItemTypeFields(type.id);
 			var baseFields = {};
-			for (let fieldID in fieldIDs) {
+			for (let fieldID of fieldIDs) {
 				if (baseMappedFields.includes(fieldID)) {
 					baseFields[fieldID] = Zotero.ItemFields.getBaseIDFromTypeAndField(type.id, fieldID);
 				}

chrome/content/zotero/xpcom/api.js

@@ -154,7 +154,7 @@ Zotero.API = {
 			return 'groups/' + Zotero.Groups.getGroupIDFromLibraryID(libraryID);
 		
 		default:
-			throw new Error(`Invalid type '${type}`);
+			throw new Error(`Invalid type '${type}'`);
 		}
 	}
 };

chrome/content/zotero/xpcom/attachments.js

@@ -40,6 +40,7 @@ Zotero.Attachments = new function(){
 	 * @param {Integer} [options.libraryID]
 	 * @param {Integer[]|String[]} [options.parentItemID] - Parent item to add item to
 	 * @param {Integer[]} [options.collections] - Collection keys or ids to add new item to
+	 * @param {String} [options.fileBaseName]
 	 * @param {String} [options.contentType]
 	 * @param {String} [options.charset]
 	 * @param {Object} [options.saveOptions] - Options to pass to Zotero.Item::save()
@@ -50,15 +51,24 @@ Zotero.Attachments = new function(){
 		
 		var libraryID = options.libraryID;
 		var file = Zotero.File.pathToFile(options.file);
+		var path = file.path;
+		var leafName = file.leafName;
 		var parentItemID = options.parentItemID;
 		var collections = options.collections;
+		var fileBaseName = options.fileBaseName;
 		var contentType = options.contentType;
 		var charset = options.charset;
 		var saveOptions = options.saveOptions;
 		
-		var newName = Zotero.File.getValidFileName(file.leafName);
+		if (fileBaseName) {
+			let ext = Zotero.File.getExtension(path);
+			var newName = fileBaseName + (ext != '' ? '.' + ext : '');
+		}
+		else {
+			var newName = Zotero.File.getValidFileName(OS.Path.basename(leafName));
+		}
 		
-		if (file.leafName.endsWith(".lnk")) {
+		if (leafName.endsWith(".lnk")) {
 			throw new Error("Cannot add Windows shortcut");
 		}
 		if (parentItemID && collections) {
@@ -95,6 +105,8 @@ Zotero.Attachments = new function(){
 				// Copy file to unique filename, which automatically shortens long filenames
 				newFile = Zotero.File.copyToUnique(file, newFile);
 				
+				yield Zotero.File.setNormalFilePermissions(newFile.path);
+				
 				if (!contentType) {
 					contentType = yield Zotero.MIME.getMIMETypeFromFile(newFile);
 				}
@@ -164,14 +176,18 @@ Zotero.Attachments = new function(){
 	
 	
 	/**
-	 * @param {Object} options - 'file', 'url', 'title', 'contentType', 'charset', 'parentItemID'
+	 * @param {Object} options - 'file', 'url', 'title', 'contentType', 'charset', 'parentItemID', 'singleFile'
 	 * @return {Promise<Zotero.Item>}
 	 */
 	this.importSnapshotFromFile = Zotero.Promise.coroutine(function* (options) {
 		Zotero.debug('Importing snapshot from file');
 		
 		var file = Zotero.File.pathToFile(options.file);
-		var fileName = file.leafName;
+		// TODO: Fix main filename when copying directory, though in that case it's probably
+		// from our own export and already clean
+		var fileName = options.singleFile
+			? Zotero.File.getValidFileName(file.leafName)
+			: file.leafName;
 		var url = options.url;
 		var title = options.title;
 		var contentType = options.contentType;
@@ -182,7 +198,7 @@ Zotero.Attachments = new function(){
 			throw new Error("parentItemID not provided");
 		}
 		
-		var attachmentItem, itemID, destDir, newFile;
+		var attachmentItem, itemID, destDir, newPath;
 		try {
 			yield Zotero.DB.executeTransaction(function* () {
 				// Create a new attachment
@@ -205,13 +221,23 @@ Zotero.Attachments = new function(){
 				var storageDir = Zotero.getStorageDirectory();
 				destDir = this.getStorageDirectory(attachmentItem);
 				yield OS.File.removeDir(destDir.path);
-				file.parent.copyTo(storageDir, destDir.leafName);
-				
-				// Point to copied file
-				newFile = destDir.clone();
-				newFile.append(file.leafName);
+				newPath = OS.Path.join(destDir.path, fileName);
+				// Copy single file to new directory
+				if (options.singleFile) {
+					yield this.createDirectoryForItem(attachmentItem);
+					yield OS.File.copy(file.path, newPath);
+				}
+				// Copy entire parent directory (for HTML snapshots)
+				else {
+					file.parent.copyTo(storageDir, destDir.leafName);
+				}
 			}.bind(this));
-			yield _postProcessFile(attachmentItem, newFile, contentType, charset);
+			yield _postProcessFile(
+				attachmentItem,
+				Zotero.File.pathToFile(newPath),
+				contentType,
+				charset
+			);
 		}
 		catch (e) {
 			Zotero.logError(e);
@@ -233,8 +259,18 @@ Zotero.Attachments = new function(){
 	
 	
 	/**
-	 * @param {Object} options - 'libraryID', 'url', 'parentItemID', 'collections', 'title',
-	 *                           'fileBaseName', 'contentType', 'cookieSandbox', 'saveOptions'
+	 * @param {Object} options
+	 * @param {Integer} options.libraryID
+	 * @param {String} options.url
+	 * @param {Integer} [options.parentItemID]
+	 * @param {Integer[]} [options.collections]
+	 * @param {String} [options.title]
+	 * @param {String} [options.fileBaseName]
+	 * @param {Boolean} [options.renameIfAllowedType=false]
+	 * @param {String} [options.contentType]
+	 * @param {String} [options.referrer]
+	 * @param {CookieSandbox} [options.cookieSandbox]
+	 * @param {Object} [options.saveOptions]
 	 * @return {Promise<Zotero.Item>} - A promise for the created attachment item
 	 */
 	this.importFromURL = Zotero.Promise.coroutine(function* (options) {
@@ -244,7 +280,9 @@ Zotero.Attachments = new function(){
 		var collections = options.collections;
 		var title = options.title;
 		var fileBaseName = options.fileBaseName;
+		var renameIfAllowedType = options.renameIfAllowedType;
 		var contentType = options.contentType;
+		var referrer = options.referrer;
 		var cookieSandbox = options.cookieSandbox;
 		var saveOptions = options.saveOptions;
 		
@@ -274,7 +312,7 @@ Zotero.Attachments = new function(){
 							if (channel.responseStatus < 200 || channel.responseStatus >= 400) {
 								reject(new Error("Invalid response " + channel.responseStatus + " "
 									+ channel.responseStatusText + " for '" + url + "'"));
-								return;
+								return false;
 							}
 						}
 						try {
@@ -306,6 +344,11 @@ Zotero.Attachments = new function(){
 		
 		// Save using remote web browser persist
 		var externalHandlerImport = Zotero.Promise.coroutine(function* (contentType) {
+			// Rename attachment
+			if (renameIfAllowedType && !fileBaseName && this.getRenamedFileTypes().includes(contentType)) {
+				let parentItem = Zotero.Items.get(parentItemID);
+				fileBaseName = this.getFileBaseNameFromItem(parentItem);
+			}
 			if (fileBaseName) {
 				let ext = _getExtensionFromURL(url, contentType);
 				var fileName = fileBaseName + (ext != '' ? '.' + ext : '');
@@ -335,7 +378,12 @@ Zotero.Attachments = new function(){
 			var nsIURL = Components.classes["@mozilla.org/network/standard-url;1"]
 				.createInstance(Components.interfaces.nsIURL);
 			nsIURL.spec = url;
-			Zotero.Utilities.Internal.saveURI(wbp, nsIURL, tmpFile);
+			var headers = {};
+			if (referrer) {
+				headers.Referer = referrer;
+			}
+			Zotero.Utilities.Internal.saveURI(wbp, nsIURL, tmpFile, headers);
+
 
 			yield deferred.promise;
 			let sample = yield Zotero.File.getContentsAsync(tmpFile, null, 1000);
@@ -375,6 +423,8 @@ Zotero.Attachments = new function(){
 					attachmentItem.attachmentPath = 'storage:' + fileName;
 					var itemID = yield attachmentItem.save(saveOptions);
 					
+					Zotero.Fulltext.queueItem(attachmentItem);
+					
 					// DEBUG: Does this fail if 'storage' is symlinked to another drive?
 					destDir = this.getStorageDirectory(attachmentItem).path;
 					yield OS.File.move(tmpDir, destDir);
@@ -394,16 +444,6 @@ Zotero.Attachments = new function(){
 				throw e;
 			}
 			
-			// We don't have any way of knowing that the file is flushed to disk,
-			// so we just wait a second before indexing and hope for the best.
-			// We'll index it later if it fails. (This may not be necessary.)
-			//
-			// If this is removed, the afterEach() delay in the server_connector /connector/saveSnapshot
-			// tests can also be removed.
-			setTimeout(function () {
-				Zotero.Fulltext.indexItems([attachmentItem.id]);
-			}, 1000);
-			
 			return attachmentItem;
 		}.bind(this));
 		
@@ -641,6 +681,8 @@ Zotero.Attachments = new function(){
 				attachmentItem.attachmentPath = 'storage:' + fileName;
 				var itemID = yield attachmentItem.save();
 				
+				Zotero.Fulltext.queueItem(attachmentItem);
+				
 				// DEBUG: Does this fail if 'storage' is symlinked to another drive?
 				destDir = this.getStorageDirectory(attachmentItem).path;
 				yield OS.File.move(tmpDir, destDir);
@@ -665,21 +707,6 @@ Zotero.Attachments = new function(){
 			throw e;
 		}
 		
-		// We don't have any way of knowing that the file is flushed to disk,
-		// so we just wait a second before indexing and hope for the best.
-		// We'll index it later if it fails. (This may not be necessary.)
-		if (contentType == 'application/pdf') {
-			setTimeout(function () {
-				Zotero.Fulltext.indexPDF(attachmentItem.getFilePath(), attachmentItem.id);
-			}, 1000);
-		}
-		else if (Zotero.MIME.isTextType(contentType)) {
-			// wbp.saveDocument consumes the document context (in Zotero.Utilities.Internal.saveDocument)
-			// Seems like a mozilla bug, but nothing on bugtracker.
-			// Either way, we don't rely on Zotero.Fulltext.indexDocument here anymore
-			yield Zotero.Fulltext.indexItems(attachmentItem.id, true, true);
-		}
-		
 		return attachmentItem;
 	});
 
@@ -785,6 +812,30 @@ Zotero.Attachments = new function(){
 	}
 	
 	
+	this.getRenamedFileTypes = function () {
+		try {
+			var types = Zotero.Prefs.get('autoRenameFiles.fileTypes');
+			return types ? types.split(',') : [];
+		}
+		catch (e) {
+			return [];
+		}
+	};
+	
+	
+	this.getRenamedFileBaseNameIfAllowedType = async function (parentItem, file) {
+		var types = this.getRenamedFileTypes();
+		var contentType = file.endsWith('.pdf')
+			// Don't bother reading file if there's a .pdf extension
+			? 'application/pdf'
+			: await Zotero.MIME.getMIMETypeFromFile(file);
+		if (!types.includes(contentType)) {
+			return false;
+		}
+		return this.getFileBaseNameFromItem(parentItem);
+	}
+	
+	
 	/**
 	 * Create directory for attachment files within storage directory
 	 *
@@ -1078,13 +1129,75 @@ Zotero.Attachments = new function(){
 	
 	
 	/**
-	 * Copy attachment item, including files, to another library
+	 * Move attachment item, including file, to another library
+	 */
+	this.moveAttachmentToLibrary = async function (attachment, libraryID, parentItemID) {
+		if (attachment.libraryID == libraryID) {
+			throw new Error("Attachment is already in library " + libraryID);
+		}
+		
+		Zotero.DB.requireTransaction();
+		
+		var newAttachment = attachment.clone(libraryID);
+		if (attachment.isImportedAttachment()) {
+			// Attachment path isn't copied over by clone() if libraryID is different
+			newAttachment.attachmentPath = attachment.attachmentPath;
+		}
+		if (parentItemID) {
+			newAttachment.parentID = parentItemID;
+		}
+		await newAttachment.save();
+		
+		// Move files over if they exist
+		var oldDir;
+		var newDir;
+		if (newAttachment.isImportedAttachment()) {
+			oldDir = this.getStorageDirectory(attachment).path;
+			if (await OS.File.exists(oldDir)) {
+				newDir = this.getStorageDirectory(newAttachment).path;
+				// Target directory shouldn't exist, but remove it if it does
+				//
+				// Testing for directories in OS.File, used by removeDir(), is broken on Travis,
+				// so use nsIFile
+				if (Zotero.automatedTest) {
+					let nsIFile = Zotero.File.pathToFile(newDir);
+					if (nsIFile.exists()) {
+						nsIFile.remove(true);
+					}
+				}
+				else {
+					await OS.File.removeDir(newDir, { ignoreAbsent: true });
+				}
+				await OS.File.move(oldDir, newDir);
+			}
+		}
+		
+		try {
+			await attachment.erase();
+		}
+		catch (e) {
+			// Move files back if old item can't be deleted
+			if (newAttachment.isImportedAttachment()) {
+				try {
+					await OS.File.move(newDir, oldDir);
+				}
+				catch (e) {
+					Zotero.logError(e);
+				}
+			}
+			throw e;
+		}
+		
+		return newAttachment.id;
+	};
+	
+	
+	/**
+	 * Copy attachment item, including file, to another library
 	 */
 	this.copyAttachmentToLibrary = Zotero.Promise.coroutine(function* (attachment, libraryID, parentItemID) {
-		var linkMode = attachment.attachmentLinkMode;
-		
 		if (attachment.libraryID == libraryID) {
-			throw ("Attachment is already in library " + libraryID);
+			throw new Error("Attachment is already in library " + libraryID);
 		}
 		
 		Zotero.DB.requireTransaction();

chrome/content/zotero/xpcom/cite.js

@@ -16,13 +16,13 @@ Zotero.Cite = {
 	 * Remove specified item IDs in-place from a citeproc-js bibliography object returned
 	 * by makeBibliography()
 	 * @param {bib} citeproc-js bibliography object
-	 * @param {Array} itemsToRemove Array of items to remove
+	 * @param {Set} itemsToRemove Set of items to remove
 	 */
 	"removeFromBibliography":function(bib, itemsToRemove) {
 		var removeItems = [];
 		for(let i in bib[0].entry_ids) {
 			for(let j in bib[0].entry_ids[i]) {
-				if(itemsToRemove[bib[0].entry_ids[i][j]]) {
+				if(itemsToRemove.has(`${bib[0].entry_ids[i][j]}`)) {
 					removeItems.push(i);
 					break;
 				}
@@ -302,7 +302,7 @@ Zotero.Cite = {
 			var sessionID = id.substr(0, slashIndex),
 				session = Zotero.Integration.sessions[sessionID],
 				item;
-			if(session) {
+			if (session) {
 				item = session.embeddedZoteroItems[id.substr(slashIndex+1)];
 			}
 			
@@ -315,6 +315,104 @@ Zotero.Cite = {
 		} else {
 			return Zotero.Items.get(id);
 		}
+	},
+	
+	extraToCSL: function (extra) {
+		return extra.replace(/^([A-Za-z \-]+)(:\s*.+)/gm, function (_, field, value) {
+			var originalField = field;
+			var field = field.toLowerCase().replace(/ /g, '-');
+			// Fields from https://aurimasv.github.io/z2csl/typeMap.xml
+			switch (field) {
+			// Standard fields
+			case 'abstract':
+			case 'accessed':
+			case 'annote':
+			case 'archive':
+			case 'archive-place':
+			case 'author':
+			case 'authority':
+			case 'call-number':
+			case 'chapter-number':
+			case 'citation-label':
+			case 'citation-number':
+			case 'collection-editor':
+			case 'collection-number':
+			case 'collection-title':
+			case 'composer':
+			case 'container':
+			case 'container-author':
+			case 'container-title':
+			case 'container-title-short':
+			case 'dimensions':
+			case 'director':
+			case 'edition':
+			case 'editor':
+			case 'editorial-director':
+			case 'event':
+			case 'event-date':
+			case 'event-place':
+			case 'first-reference-note-number':
+			case 'genre':
+			case 'illustrator':
+			case 'interviewer':
+			case 'issue':
+			case 'issued':
+			case 'jurisdiction':
+			case 'keyword':
+			case 'language':
+			case 'locator':
+			case 'medium':
+			case 'note':
+			case 'number':
+			case 'number-of-pages':
+			case 'number-of-volumes':
+			case 'original-author':
+			case 'original-date':
+			case 'original-publisher':
+			case 'original-publisher-place':
+			case 'original-title':
+			case 'page':
+			case 'page-first':
+			case 'publisher':
+			case 'publisher-place':
+			case 'recipient':
+			case 'references':
+			case 'reviewed-author':
+			case 'reviewed-title':
+			case 'scale':
+			case 'section':
+			case 'source':
+			case 'status':
+			case 'submitted':
+			case 'title':
+			case 'title-short':
+			case 'translator':
+			case 'version':
+			case 'volume':
+			case 'year-suffix':
+				break;
+			
+			// Uppercase fields
+			case 'doi':
+			case 'isbn':
+			case 'issn':
+			case 'pmcid':
+			case 'pmid':
+			case 'url':
+				field = field.toUpperCase();
+				break;
+			
+			// Weirdo
+			case 'archive-location':
+				field = 'archive_location';
+				break;
+			
+			// Don't change other lines
+			default:
+				field = originalField;
+			}
+			return field + value;
+		});
 	}
 };
 
@@ -498,7 +596,7 @@ Zotero.Cite.System.prototype = {
 	/**
 	 * citeproc-js system function for getting items
 	 * See http://gsl-nagoya-u.net/http/pub/citeproc-doc.html#retrieveitem
-	 * @param {String|Integer} Item ID, or string item for embedded citations
+	 * @param {String|Integer} item - Item ID, or string item for embedded citations
 	 * @return {Object} citeproc-js item
 	 */
 	"retrieveItem":function retrieveItem(item) {
@@ -509,10 +607,10 @@ Zotero.Cite.System.prototype = {
 		} else if(typeof item === "string" && (slashIndex = item.indexOf("/")) !== -1) {
 			// is an embedded item
 			var sessionID = item.substr(0, slashIndex);
-			var session = Zotero.Integration.sessions[sessionID]
+			var session = Zotero.Integration.sessions[sessionID];
 			if(session) {
 				var embeddedCitation = session.embeddedItems[item.substr(slashIndex+1)];
-				if(embeddedCitation) {
+				if (embeddedCitation) {
 					embeddedCitation.id = item;
 					return embeddedCitation;
 				}
@@ -526,7 +624,7 @@ Zotero.Cite.System.prototype = {
 		}
 
 		if(!zoteroItem) {
-			throw "Zotero.Cite.System.retrieveItem called on non-item "+item;
+			throw new Error("Zotero.Cite.System.retrieveItem called on non-item "+item);
 		}
 		
 		var cslItem = Zotero.Utilities.itemToCSLJSON(zoteroItem);

chrome/content/zotero/xpcom/collectionTreeRow.js

@@ -381,8 +381,8 @@ Zotero.CollectionTreeRow.prototype.getChildTags = Zotero.Promise.coroutine(funct
 		case 'bucket':
 			return [];
 	}
-	var results = yield this.getSearchResults();
-	return Zotero.Tags.getAllWithinItemsList(results);
+	var results = yield this.getSearchResults(true);
+	return Zotero.Tags.getAllWithinSearchResults(results);
 });
 
 

chrome/content/zotero/xpcom/collectionTreeView.js

@@ -76,6 +76,14 @@ Object.defineProperty(Zotero.CollectionTreeView.prototype, "selectedTreeRow", {
 });
 
 
+Object.defineProperty(Zotero.CollectionTreeView.prototype, 'window', {
+	get: function () {
+		return this._ownerDocument.defaultView;
+	},
+	enumerable: true
+});
+
+
 /*
  *  Called by the tree itself
  */
@@ -87,6 +95,13 @@ Zotero.CollectionTreeView.prototype.setTree = Zotero.Promise.coroutine(function*
 		}
 		this._treebox = treebox;
 		
+		if (!this._ownerDocument) {
+			try {
+				this._ownerDocument = treebox.treeBody.ownerDocument;
+			}
+			catch (e) {}
+		}
+		
 		// Add a keypress listener for expand/collapse
 		var tree = this._treebox.treeBody.parentNode;
 		tree.addEventListener('keypress', function(event) {
@@ -1606,6 +1621,7 @@ Zotero.CollectionTreeView.prototype.canDropCheck = function (row, orient, dataTr
 		if (dataType == 'zotero/item') {
 			var ids = data;
 			var items = Zotero.Items.get(ids);
+			items = Zotero.Items.keepParents(items);
 			var skip = true;
 			for (let item of items) {
 				// Can only drag top-level items
@@ -1813,6 +1829,7 @@ Zotero.CollectionTreeView.prototype.canDropCheckAsync = Zotero.Promise.coroutine
 			if (treeRow.ref.libraryID != draggedCollection.libraryID) {
 				// Disallow if linked collection already exists
 				if (yield draggedCollection.getLinkedCollection(treeRow.ref.libraryID, true)) {
+					Zotero.debug("Linked collection already exists in library");
 					return false;
 				}
 				
@@ -1824,6 +1841,7 @@ Zotero.CollectionTreeView.prototype.canDropCheckAsync = Zotero.Promise.coroutine
 					// If this is allowed in the future for the root collection,
 					// need to allow drag only to root
 					if (yield descendent.getLinkedCollection(treeRow.ref.libraryID, true)) {
+						Zotero.debug("Linked subcollection already exists in library");
 						return false;
 					}
 				}
@@ -2115,6 +2133,7 @@ Zotero.CollectionTreeView.prototype.drop = Zotero.Promise.coroutine(function* (r
 		}
 		
 		if (targetTreeRow.isPublications()) {
+			items = Zotero.Items.keepParents(items);
 			let io = this._treebox.treeBody.ownerDocument.defaultView
 				.ZoteroPane.showPublicationsWizard(items);
 			if (!io) {
@@ -2186,9 +2205,7 @@ Zotero.CollectionTreeView.prototype.drop = Zotero.Promise.coroutine(function* (r
 				}
 				*/
 				
-				let wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-						   .getService(Components.interfaces.nsIWindowMediator);
-				let lastWin = wm.getMostRecentWindow("navigator:browser");
+				let lastWin = Services.wm.getMostRecentWindow("navigator:browser");
 				lastWin.openDialog('chrome://zotero/content/merge.xul', '', 'chrome,modal,centerscreen', io);
 				
 				yield Zotero.DB.executeTransaction(function* () {
@@ -2227,24 +2244,23 @@ Zotero.CollectionTreeView.prototype.drop = Zotero.Promise.coroutine(function* (r
 	}
 	else if (dataType == 'text/x-moz-url' || dataType == 'application/x-moz-file') {
 		var targetLibraryID = targetTreeRow.ref.libraryID;
-		
 		if (targetTreeRow.isCollection()) {
 			var parentCollectionID = targetTreeRow.ref.id;
 		}
 		else {
 			var parentCollectionID = false;
 		}
+		var addedItems = [];
 		
 		for (var i=0; i<data.length; i++) {
 			var file = data[i];
 			
 			if (dataType == 'text/x-moz-url') {
 				var url = data[i];
+				let item;
 				
 				if (url.indexOf('file:///') == 0) {
-					var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-							   .getService(Components.interfaces.nsIWindowMediator);
-					var win = wm.getMostRecentWindow("navigator:browser");
+					let win = Services.wm.getMostRecentWindow("navigator:browser");
 					// If dragging currently loaded page, only convert to
 					// file if not an HTML document
 					if (win.content.location.href != url ||
@@ -2262,9 +2278,7 @@ Zotero.CollectionTreeView.prototype.drop = Zotero.Promise.coroutine(function* (r
 				
 				// Still string, so remote URL
 				if (typeof file == 'string') {
-					var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-							   .getService(Components.interfaces.nsIWindowMediator);
-					var win = wm.getMostRecentWindow("navigator:browser");
+					let win = Services.wm.getMostRecentWindow("navigator:browser");
 					win.ZoteroPane.addItemFromURL(url, 'temporaryPDFHack', null, row); // TODO: don't do this
 					continue;
 				}
@@ -2273,13 +2287,13 @@ Zotero.CollectionTreeView.prototype.drop = Zotero.Promise.coroutine(function* (r
 			}
 			
 			if (dropEffect == 'link') {
-				yield Zotero.Attachments.linkFromFile({
+				item = yield Zotero.Attachments.linkFromFile({
 					file: file,
 					collections: parentCollectionID ? [parentCollectionID] : undefined
 				});
 			}
 			else {
-				yield Zotero.Attachments.importFromFile({
+				item = yield Zotero.Attachments.importFromFile({
 					file: file,
 					libraryID: targetLibraryID,
 					collections: parentCollectionID ? [parentCollectionID] : undefined
@@ -2294,7 +2308,12 @@ Zotero.CollectionTreeView.prototype.drop = Zotero.Promise.coroutine(function* (r
 					}
 				}
 			}
+			
+			addedItems.push(item);
 		}
+		
+		// Automatically retrieve metadata for PDFs
+		Zotero.RecognizePDF.autoRecognizeItems(addedItems);
 	}
 });
 
@@ -2359,11 +2378,12 @@ Zotero.CollectionTreeCache = {
 	"clear": function () {
 		this.lastTreeRow = null;
 		this.lastSearch = null;
-		if(this.lastTempTable) {
-			// Drop the last temp table when we can. We don't wait on this because it can cause a
-			// deadlock: this waits on open transactions, but a transaction could be waiting on
-			// ItemTreeView::notify(), which waits on ItemTreeView::refresh(), which calls this.
-			Zotero.DB.queryTx("DROP TABLE IF EXISTS " + this.lastTempTable).done();
+		if (this.lastTempTable) {
+			let tableName = this.lastTempTable;
+			let id = Zotero.DB.addCallback('commit', async function () {
+				await Zotero.DB.queryAsync("DROP TABLE IF EXISTS " + tableName);
+				Zotero.DB.removeCallback('commit', id);
+			});
 		}
 		this.lastTempTable = null;
 		this.lastResults = null;

chrome/content/zotero/xpcom/connector/httpIntegrationClient.js

@@ -0,0 +1,192 @@
+/*
+	***** BEGIN LICENSE BLOCK *****
+	
+	Copyright © 2017 Center for History and New Media
+					George Mason University, Fairfax, Virginia, USA
+					http://zotero.org
+	
+	This file is part of Zotero.
+	
+	Zotero is free software: you can redistribute it and/or modify
+	it under the terms of the GNU Affero General Public License as published by
+	the Free Software Foundation, either version 3 of the License, or
+	(at your option) any later version.
+	
+	Zotero is distributed in the hope that it will be useful,
+	but WITHOUT ANY WARRANTY; without even the implied warranty of
+	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	GNU Affero General Public License for more details.
+
+	You should have received a copy of the GNU Affero General Public License
+	along with Zotero.  If not, see <http://www.gnu.org/licenses/>.
+	
+	***** END LICENSE BLOCK *****
+*/
+
+/**
+ * This is a HTTP-based integration interface for Zotero. The actual
+ * heavy lifting occurs in the connector and/or wherever the connector delegates the heavy
+ * lifting to.
+ */
+Zotero.HTTPIntegrationClient = {
+	deferredResponse: null,
+	sendCommandPromise: Zotero.Promise.resolve(),
+	sendCommand: async function(command, args=[]) {
+		let payload = JSON.stringify({command, arguments: args});
+		function sendCommand() {
+			Zotero.HTTPIntegrationClient.deferredResponse = Zotero.Promise.defer();
+			Zotero.HTTPIntegrationClient.sendResponse.apply(Zotero.HTTPIntegrationClient,
+				[200, 'application/json', payload]);
+			return Zotero.HTTPIntegrationClient.deferredResponse.promise;
+		}
+		// Force issued commands to occur sequentially, since these are really just
+		// a sequence of HTTP requests and responses.
+		// We might want to consider something better later, but this has the advantage of
+		// being easy to interface with as a Client, as you don't need SSE or WS.
+		if (command != 'Document.complete') {
+			Zotero.HTTPIntegrationClient.sendCommandPromise = 
+				Zotero.HTTPIntegrationClient.sendCommandPromise.then(sendCommand, sendCommand);
+		} else {
+			await Zotero.HTTPIntegrationClient.sendCommandPromise;
+			sendCommand();
+		}
+		return Zotero.HTTPIntegrationClient.sendCommandPromise;
+	}
+};
+
+Zotero.HTTPIntegrationClient.Application = function() {
+	this.primaryFieldType = "Http";
+	this.secondaryFieldType = "Http";
+	this.outputFormat = 'html';
+	this.supportedNotes = ['footnotes'];
+};
+Zotero.HTTPIntegrationClient.Application.prototype = {
+	getActiveDocument: async function() {
+		let result = await Zotero.HTTPIntegrationClient.sendCommand('Application.getActiveDocument');
+		this.outputFormat = result.outputFormat || this.outputFormat;
+		this.supportedNotes = result.supportedNotes || this.supportedNotes;
+		return new Zotero.HTTPIntegrationClient.Document(result.documentID);
+	}
+};
+
+/**
+ * See integrationTests.js
+ */
+Zotero.HTTPIntegrationClient.Document = function(documentID) {
+	this._documentID = documentID;
+};
+for (let method of ["activate", "canInsertField", "displayAlert", "getDocumentData",
+	"setDocumentData", "setBibliographyStyle"]) {
+	Zotero.HTTPIntegrationClient.Document.prototype[method] = async function() {
+		return Zotero.HTTPIntegrationClient.sendCommand("Document."+method,
+			[this._documentID].concat(Array.prototype.slice.call(arguments)));
+	};
+}
+
+// @NOTE Currently unused, prompts are done using the connector
+Zotero.HTTPIntegrationClient.Document.prototype._displayAlert = async function(dialogText, icon, buttons) {
+	var ps = Services.prompt;
+	var buttonFlags = (ps.BUTTON_POS_0) * (ps.BUTTON_TITLE_OK)
+		+ (ps.BUTTON_POS_1) * (ps.BUTTON_TITLE_IS_STRING);
+	
+	switch (buttons) {
+		case DIALOG_BUTTONS_OK:
+			buttonFlags = ps.BUTTON_POS_0_DEFAULT + ps.BUTTON_POS_0 * ps.BUTTON_TITLE_OK; break;
+		case DIALOG_BUTTONS_OK_CANCEL:
+			buttonFlags = ps.BUTTON_POS_0_DEFAULT + ps.STD_OK_CANCEL_BUTTONS; break;
+		case DIALOG_BUTTONS_YES_NO:
+			buttonFlags = ps.BUTTON_POS_0_DEFAULT + ps.STD_YES_NO_BUTTONS; break;
+		case DIALOG_BUTTONS_YES_NO_CANCEL:
+			buttonFlags = ps.BUTTON_POS_0_DEFAULT + ps.BUTTON_POS_0 * ps.BUTTON_TITLE_YES +
+				ps.BUTTON_POS_1 * ps.BUTTON_TITLE_NO +
+				ps.BUTTON_POS_2 * ps.BUTTON_TITLE_CANCEL; break;
+	}
+
+	var result = ps.confirmEx(
+		null,
+		"Zotero",
+		dialogText,
+		buttonFlags,
+		null, null, null,
+		null,
+		{}
+	);
+	
+	switch (buttons) {
+		default:
+			break;
+		case DIALOG_BUTTONS_OK_CANCEL:
+		case DIALOG_BUTTONS_YES_NO:
+			result = (result+1)%2; break;
+		case DIALOG_BUTTONS_YES_NO_CANCEL:
+			result = result == 0 ? 2 : result == 2 ? 0 : 1; break;
+	}
+	await this.activate();
+	return result;
+}
+Zotero.HTTPIntegrationClient.Document.prototype.cleanup = async function() {};
+Zotero.HTTPIntegrationClient.Document.prototype.cursorInField = async function(fieldType) {
+	var retVal = await Zotero.HTTPIntegrationClient.sendCommand("Document.cursorInField", [this._documentID, fieldType]);
+	if (!retVal) return null;
+	return new Zotero.HTTPIntegrationClient.Field(this._documentID, retVal);
+};
+Zotero.HTTPIntegrationClient.Document.prototype.insertField = async function(fieldType, noteType) {
+	var retVal = await Zotero.HTTPIntegrationClient.sendCommand("Document.insertField", [this._documentID, fieldType, parseInt(noteType) || 0]);
+	return new Zotero.HTTPIntegrationClient.Field(this._documentID, retVal);
+};
+Zotero.HTTPIntegrationClient.Document.prototype.getFields = async function(fieldType) {
+	var retVal = await Zotero.HTTPIntegrationClient.sendCommand("Document.getFields", [this._documentID, fieldType]);
+	return retVal.map(field => new Zotero.HTTPIntegrationClient.Field(this._documentID, field));
+};
+Zotero.HTTPIntegrationClient.Document.prototype.convert = async function(fields, fieldType, noteTypes) {
+	fields = fields.map((f) => f._id);
+	await Zotero.HTTPIntegrationClient.sendCommand("Field.convert", [this._documentID, fields, fieldType, noteTypes]);
+};
+Zotero.HTTPIntegrationClient.Document.prototype.complete = async function() {
+	Zotero.HTTPIntegrationClient.inProgress = false;
+	Zotero.HTTPIntegrationClient.sendCommand("Document.complete", [this._documentID]);
+};
+
+/**
+ * See integrationTests.js
+ */
+Zotero.HTTPIntegrationClient.Field = function(documentID, json) {
+	this._documentID = documentID; 
+	this._id = json.id;
+	this._code = json.code;
+	this._text = json.text;
+	this._noteIndex = json.noteIndex;
+};
+Zotero.HTTPIntegrationClient.Field.prototype = {};
+
+for (let method of ["delete", "select", "removeCode"]) {
+	Zotero.HTTPIntegrationClient.Field.prototype[method] = async function() {
+		return Zotero.HTTPIntegrationClient.sendCommand("Field."+method,
+			[this._documentID, this._id].concat(Array.prototype.slice.call(arguments)));
+	};
+}
+Zotero.HTTPIntegrationClient.Field.prototype.getText = async function() {
+	return this._text;
+};
+Zotero.HTTPIntegrationClient.Field.prototype.setText = async function(text, isRich) {
+	// The HTML will be stripped by Google Docs and and since we're 
+	// caching this value, we need to strip it ourselves
+	var parser = Components.classes["@mozilla.org/xmlextras/domparser;1"]
+             .createInstance(Components.interfaces.nsIDOMParser);
+	var doc = parser.parseFromString(text, "text/html");
+	this._text = doc.documentElement.textContent;
+	return Zotero.HTTPIntegrationClient.sendCommand("Field.setText", [this._documentID, this._id, text, true]);
+};
+Zotero.HTTPIntegrationClient.Field.prototype.getCode = async function() {
+	return this._code;
+};
+Zotero.HTTPIntegrationClient.Field.prototype.setCode = async function(code) {
+	this._code = code;
+	return Zotero.HTTPIntegrationClient.sendCommand("Field.setCode", [this._documentID, this._id, code]);
+};
+Zotero.HTTPIntegrationClient.Field.prototype.getNoteIndex = async function() {
+	return this._noteIndex;
+};
+Zotero.HTTPIntegrationClient.Field.prototype.equals = async function(arg) {
+	return this._id === arg._id;
+};

chrome/content/zotero/xpcom/connector/server_connectorIntegration.js

@@ -0,0 +1,83 @@
+/*
+	***** BEGIN LICENSE BLOCK *****
+	
+	Copyright © 2017 Center for History and New Media
+					George Mason University, Fairfax, Virginia, USA
+					http://zotero.org
+	
+	This file is part of Zotero.
+	
+	Zotero is free software: you can redistribute it and/or modify
+	it under the terms of the GNU Affero General Public License as published by
+	the Free Software Foundation, either version 3 of the License, or
+	(at your option) any later version.
+	
+	Zotero is distributed in the hope that it will be useful,
+	but WITHOUT ANY WARRANTY; without even the implied warranty of
+	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+	GNU Affero General Public License for more details.
+
+	You should have received a copy of the GNU Affero General Public License
+	along with Zotero.  If not, see <http://www.gnu.org/licenses/>.
+	
+	***** END LICENSE BLOCK *****
+*/
+
+/**
+ * Adds integration endpoints related to doc integration via HTTP/connector.
+ * 
+ * document/execCommand initiates an integration command and responds with the
+ * next request for the http client (e.g. 'Application.getDocument').
+ * The client should respond to document/respond with the payload and expect
+ * another response with the next request, until it receives 'Document.complete'
+ * at which point the integration transaction is considered complete.
+ */
+Zotero.Server.Endpoints['/connector/document/execCommand'] = function() {};
+Zotero.Server.Endpoints['/connector/document/execCommand'].prototype = {
+	supportedMethods: ["POST"],
+	supportedDataTypes: ["application/json"],
+	permitBookmarklet: true,
+	init: function(data, sendResponse) {
+		if (Zotero.HTTPIntegrationClient.inProgress) {
+			// This will focus the last integration window if present
+			Zotero.Integration.execCommand('http', data.command, data.docId);
+			sendResponse(503, 'text/plain', 'Integration transaction is already in progress')
+			return;
+		}
+		Zotero.HTTPIntegrationClient.inProgress = true;
+		Zotero.HTTPIntegrationClient.sendResponse = sendResponse;
+		Zotero.Integration.execCommand('http', data.command, data.docId);
+	},
+};
+
+Zotero.Server.Endpoints['/connector/document/respond'] = function() {};
+Zotero.Server.Endpoints['/connector/document/respond'].prototype = {
+	supportedMethods: ["POST"],
+	supportedDataTypes: ["application/json"],
+	permitBookmarklet: true,
+	
+	init: function(data, sendResponse) {
+		data = JSON.parse(data);
+		if (data && data.error) {
+			// Apps Script stack is a JSON object
+			if (typeof data.stack != "string") {
+				data.stack = JSON.stringify(data.stack);
+			}
+			Zotero.HTTPIntegrationClient.deferredResponse.reject(data);
+		} else {
+			Zotero.HTTPIntegrationClient.deferredResponse.resolve(data);
+		}
+		Zotero.HTTPIntegrationClient.sendResponse = sendResponse;
+	}
+};
+
+// For managing macOS integration and progress window focus
+Zotero.Server.Endpoints['/connector/sendToBack'] = function() {};
+Zotero.Server.Endpoints['/connector/sendToBack'].prototype = {
+	supportedMethods: ["POST"],
+	supportedDataTypes: ["application/json"],
+	permitBookmarklet: true,
+	init: function() {
+		Zotero.Utilities.Internal.sendToBack();
+	},
+};

chrome/content/zotero/xpcom/data/cachedTypes.js

@@ -219,7 +219,6 @@ Zotero.CreatorTypes = new function() {
 	Zotero.CachedTypes.apply(this, arguments);
 	this.constructor.prototype = new Zotero.CachedTypes();
 	
-	this.getTypesForItemType = getTypesForItemType;
 	this.isValidForItemType = isValidForItemType;
 	
 	this._typeDesc = 'creator type';
@@ -237,11 +236,8 @@ Zotero.CreatorTypes = new function() {
 	this.init = Zotero.Promise.coroutine(function* () {
 		yield this.constructor.prototype.init.apply(this);
 		
-		var sql = "SELECT itemTypeID, creatorTypeID AS id, creatorType AS name "
-			+ "FROM itemTypeCreatorTypes NATURAL JOIN creatorTypes "
-			// DEBUG: sort needs to be on localized strings in itemPane.js
-			// (though still put primary field at top)
-			+ "ORDER BY primaryField=1 DESC, name";
+		var sql = "SELECT itemTypeID, creatorTypeID AS id, creatorType AS name, primaryField "
+			+ "FROM itemTypeCreatorTypes NATURAL JOIN creatorTypes";
 		var rows = yield Zotero.DB.queryAsync(sql);
 		for (let i=0; i<rows.length; i++) {
 			let row = rows[i];
@@ -251,7 +247,20 @@ Zotero.CreatorTypes = new function() {
 			}
 			_creatorTypesByItemType[itemTypeID].push({
 				id: row.id,
-				name: row.name
+				name: row.name,
+				primaryField: row.primaryField,
+				localizedName: this.getLocalizedString(row.name)
+			});
+		}
+		// Sort primary field first, then by localized name
+		for (let itemTypeID in _creatorTypesByItemType) {
+			_creatorTypesByItemType[itemTypeID].sort((a, b) => {
+				if (a.primaryField != b.primaryField) return b.primaryField - a.primaryField;
+				return Zotero.localeCompare(a.localizedName, b.localizedName);
+			});
+			_creatorTypesByItemType[itemTypeID].forEach((x) => {
+				delete x.primaryField;
+				delete x.localizedName;
 			});
 		}
 		
@@ -267,11 +276,10 @@ Zotero.CreatorTypes = new function() {
 	});
 	
 	
-	function getTypesForItemType(itemTypeID) {
+	this.getTypesForItemType = function (itemTypeID) {
 		if (!_creatorTypesByItemType[itemTypeID]) {
-			throw new Error("Creator types not loaded for itemTypeID " + itemTypeID);
+			return [];
 		}
-		
 		return _creatorTypesByItemType[itemTypeID];
 	}
 	
@@ -451,44 +459,44 @@ Zotero.ItemTypes = new function() {
 			
 			// HiDPI images available
 			case 'attachment-link':
+			case 'attachment-pdf':
 			case 'attachment-web-link':
 			case 'artwork':
 			case 'audioRecording':
 			case 'bill':
+			case 'blogPost':
 			case 'book':
 			case 'bookSection':
+			case 'case':
 			case 'computerProgram':
+			case 'dictionaryEntry':
+			case 'email':
+			case 'encyclopediaArticle':
 			case 'film':
 			case 'forumPost':
+			case 'hearing':
 			case 'instantMessage':
 			case 'interview':
 			case 'journalArticle':
 			case 'letter':
 			case 'magazineArticle':
+			case 'manuscript':
 			case 'newspaperArticle':
 			case 'note':
+			case 'patent':
+			case 'presentation':
 			case 'report':
+			case 'statute':
+			case 'thesis':
 			case 'webpage':
 				return "chrome://zotero/skin/treeitem-" + itemType + suffix + ".png";
 			
 			// No HiDPI images available
 			case 'attachment-snapshot':
-			case 'attachment-pdf':
-			case 'blogPost':
-			case 'case':
 			case 'conferencePaper':
-			case 'dictionaryEntry':
-			case 'email':
-			case 'encyclopediaArticle':
-			case 'hearing':
-			case 'manuscript':
 			case 'map':
-			case 'patent':
 			case 'podcast':
-			case 'presentation':
 			case 'radioBroadcast':
-			case 'statute':
-			case 'thesis':
 			case 'tvBroadcast':
 			case 'videoRecording':
 				return "chrome://zotero/skin/treeitem-" + itemType + ".png";

chrome/content/zotero/xpcom/data/collection.js

@@ -698,8 +698,7 @@ Zotero.Collection.prototype.fromJSON = function (json) {
 	this.name = json.name;
 	this.parentKey = json.parentCollection ? json.parentCollection : false;
 	
-	// TODO
-	//this.setRelations(json.relations);
+	this.setRelations(json.relations || {});
 }
 
 
@@ -713,7 +712,7 @@ Zotero.Collection.prototype.toJSON = function (options = {}) {
 	
 	obj.name = this.name;
 	obj.parentCollection = this.parentKey ? this.parentKey : false;
-	obj.relations = {}; // TEMP
+	obj.relations = this.getRelations();
 	
 	return this._postToJSON(env);
 }

chrome/content/zotero/xpcom/data/creators.js

@@ -31,16 +31,33 @@ Zotero.Creators = new function() {
 	var _cache = {};
 	
 	this.init = Zotero.Promise.coroutine(function* () {
+		var repaired = false;
 		var sql = "SELECT * FROM creators";
 		var rows = yield Zotero.DB.queryAsync(sql);
 		for (let i = 0; i < rows.length; i++) {
 			let row = rows[i];
-			_cache[row.creatorID] = this.cleanData({
-				// Avoid "DB column 'name' not found" warnings from the DB row Proxy
-				firstName: row.firstName,
-				lastName: row.lastName,
-				fieldMode: row.fieldMode
-			});
+			try {
+				_cache[row.creatorID] = this.cleanData({
+					// Avoid "DB column 'name' not found" warnings from the DB row Proxy
+					firstName: row.firstName,
+					lastName: row.lastName,
+					fieldMode: row.fieldMode
+				});
+			}
+			catch (e) {
+				// Automatically fix DB errors and try again
+				if (!repaired) {
+					Zotero.logError(e);
+					Zotero.logError("Trying integrity check to fix creator error");
+					yield Zotero.Schema.integrityCheck(true);
+					repaired = true;
+					rows = yield Zotero.DB.queryAsync(sql);
+					i = -1;
+					continue;
+				}
+				
+				throw e;
+			}
 		}
 	});
 	

chrome/content/zotero/xpcom/data/dataCache.js

@@ -0,0 +1,5 @@
+"use strict";
+
+Zotero.DataCache = {
+	
+};

chrome/content/zotero/xpcom/data/dataObject.js

@@ -285,7 +285,7 @@ Zotero.DataObject.prototype._setParentKey = function(key) {
 /**
  * Returns all relations of the object
  *
- * @return {Object} - Object with predicates as keys and arrays of URIs as values
+ * @return {Object} - Object with predicates as keys and arrays of values
  */
 Zotero.DataObject.prototype.getRelations = function () {
 	this._requireData('relations');
@@ -410,7 +410,7 @@ Zotero.DataObject.prototype.setRelations = function (newRelations) {
 	
 	// Limit predicates to letters and colons for now
 	for (let p in newRelations) {
-		if (!/[a-z]+:[a-z]+/.test(p)) {
+		if (!/^[a-z]+:[a-z]+$/i.test(p)) {
 			throw new Error(`Invalid relation predicate '${p}'`);
 		}
 	}
@@ -1249,15 +1249,19 @@ Zotero.DataObject.prototype._finalizeErase = Zotero.Promise.coroutine(function*
 });
 
 
-Zotero.DataObject.prototype.toResponseJSON = function (options) {
+Zotero.DataObject.prototype.toResponseJSON = function (options = {}) {
 	// TODO: library block?
 	
-	return {
+	var json = {
 		key: this.key,
 		version: this.version,
 		meta: {},
 		data: this.toJSON(options)
 	};
+	if (options.version) {
+		json.version = json.data.version = options.version;
+	}
+	return json;
 }
 
 
@@ -1285,6 +1289,9 @@ Zotero.DataObject.prototype._postToJSON = function (env) {
 	if (env.mode == 'patch') {
 		env.obj = Zotero.DataObjectUtilities.patch(env.options.patchBase, env.obj);
 	}
+	if (env.options.includeVersion === false) {
+		delete env.obj.version;
+	}
 	return env.obj;
 }
 

chrome/content/zotero/xpcom/data/dataObjectUtilities.js

@@ -234,14 +234,9 @@ Zotero.DataObjectUtilities = {
 	},
 	
 	_conditionsChanged: function (data1, data2) {
-		if (!data2) return true;
-		var pred1 = Object.keys(data1);
-		pred1.sort();
-		var pred2 = Object.keys(data2);
-		pred2.sort();
-		if (!Zotero.Utilities.arrayEquals(pred1, pred2)) return false;
-		for (let i in pred1) {
-			if (!Zotero.Utilities.arrayEquals(pred1[i], pred2[i])) {
+		if (!data2 || data1.length != data2.length) return true;
+		for (let i = 0; i < data1.length; i++) {
+			if (!Zotero.Searches.conditionEquals(data1[i], data2[i])) {
 				return true;
 			}
 		}

chrome/content/zotero/xpcom/data/dataObjects.js

@@ -231,6 +231,12 @@ Zotero.DataObjects.prototype.getLoaded = function () {
 }
 
 
+Zotero.DataObjects.prototype.getAllIDs = function (libraryID) {
+	var sql = `SELECT ${this._ZDO_id} FROM ${this._ZDO_table} WHERE libraryID=?`;
+	return Zotero.DB.columnQueryAsync(sql, [libraryID]);
+};
+
+
 Zotero.DataObjects.prototype.getAllKeys = function (libraryID) {
 	var sql = "SELECT key FROM " + this._ZDO_table + " WHERE libraryID=?";
 	return Zotero.DB.columnQueryAsync(sql, [libraryID]);
@@ -319,6 +325,11 @@ Zotero.DataObjects.prototype.exists = function (id) {
 }
 
 
+Zotero.DataObjects.prototype.existsByKey = function (key) {
+	return !!this.getIDFromLibraryAndKey(id);
+}
+
+
 /**
  * @return {Object} Object with 'libraryID' and 'key'
  */

chrome/content/zotero/xpcom/data/feed.js

@@ -111,6 +111,10 @@ Zotero.defineProperty(Zotero.Feed.prototype, 'isFeed', {
 	value: true
 });
 
+Zotero.defineProperty(Zotero.Feed.prototype, 'allowsLinkedFiles', {
+	value: false
+});
+
 Zotero.defineProperty(Zotero.Feed.prototype, 'libraryTypes', {
 	value: Object.freeze(Zotero.Feed._super.prototype.libraryTypes.concat(['feed']))
 });

chrome/content/zotero/xpcom/data/feedItem.js

@@ -203,8 +203,8 @@ Zotero.FeedItem.prototype.toggleRead = Zotero.Promise.coroutine(function* (state
  * Uses the item url to translate an existing feed item.
  * If libraryID empty, overwrites feed item, otherwise saves
  * in the library
- * @param libraryID {int} save item in library
- * @param collectionID {int} add item to collection
+ * @param libraryID {Integer} save item in library
+ * @param collectionID {Integer} add item to collection
  * @return {Promise<FeedItem|Item>} translated feed item
  */
 Zotero.FeedItem.prototype.translate = Zotero.Promise.coroutine(function* (libraryID, collectionID) {
@@ -254,23 +254,7 @@ Zotero.FeedItem.prototype.translate = Zotero.Promise.coroutine(function* (librar
 	if (!translators || !translators.length) {
 		Zotero.debug("No translators detected for feed item " + this.id + " with URL " + this.getField('url') + 
 			' -- cloning item instead', 2);
-		let dbItem = this.clone(libraryID);
-		if (collectionID) {
-			dbItem.addToCollection(collectionID);
-		}
-		yield dbItem.saveTx();
-		
-		let item = {title: dbItem.getField('title'), itemType: dbItem.itemType};
-		
-		// Add snapshot
-		if (Zotero.Libraries.get(libraryID).filesEditable) {
-			item.attachments = [{title: "Snapshot"}];
-			yield Zotero.Attachments.importFromDocument({
-				document: doc,
-				parentItemID: dbItem.id
-			});
-		}
-		
+		let item = yield this.clone(libraryID, collectionID, doc);
 		progressWindow.Translation.itemDoneHandler()(null, null, item);
 		progressWindow.Translation.doneHandler(null, true);
 		return;
@@ -283,6 +267,12 @@ Zotero.FeedItem.prototype.translate = Zotero.Promise.coroutine(function* (librar
 		let result = yield translate.translate({libraryID, collections: collectionID ? [collectionID] : false})
 			.then(items => items ? items[0] : false);
 		Zotero.Browser.deleteHiddenBrowser(hiddenBrowser);
+		if (!result) {
+			let item = yield this.clone(libraryID, collectionID, doc);
+			progressWindow.Translation.itemDoneHandler()(null, null, item);
+			progressWindow.Translation.doneHandler(null, true);
+			return;
+		}
 		return result;
 	}
 	
@@ -309,3 +299,30 @@ Zotero.FeedItem.prototype.translate = Zotero.Promise.coroutine(function* (librar
 	
 	return this;
 });
+
+/**
+ * Clones the feed item (usually, when proper translation is unavailable)
+ * @param libraryID {Integer} save item in library
+ * @param collectionID {Integer} add item to collection
+ * @return {Promise<FeedItem|Item>} translated feed item
+ */
+Zotero.FeedItem.prototype.clone = Zotero.Promise.coroutine(function* (libraryID, collectionID, doc) {
+	let dbItem = Zotero.Item.prototype.clone.call(this, libraryID);
+	if (collectionID) {
+		dbItem.addToCollection(collectionID);
+	}
+	yield dbItem.saveTx();
+	
+	let item = {title: dbItem.getField('title'), itemType: dbItem.itemType, attachments: []};
+	
+	// Add snapshot
+	if (Zotero.Libraries.get(libraryID).filesEditable) {
+		item.attachments = [{title: "Snapshot"}];
+		yield Zotero.Attachments.importFromDocument({
+			document: doc,
+			parentItemID: dbItem.id
+		});
+	}
+	
+	return item;
+});

chrome/content/zotero/xpcom/data/group.js

@@ -86,6 +86,10 @@ Zotero.defineProperty(Zotero.Group.prototype, 'id', {
 	set: function(v) { return this.groupID = v; }
 });
 
+Zotero.defineProperty(Zotero.Group.prototype, 'allowsLinkedFiles', {
+	value: false
+});
+
 // Create accessors
 (function() {
 let accessors = ['name', 'description', 'version'];

chrome/content/zotero/xpcom/data/item.js

@@ -145,6 +145,9 @@ Zotero.defineProperty(Zotero.Item.prototype, 'parentItemKey', {
 	get: function() { return this.parentKey; },
 	set: function(val) { return this.parentKey = val; }
 });
+Zotero.defineProperty(Zotero.Item.prototype, 'parentItem', {
+	get: function() { return Zotero.Items.get(this.parentID) || undefined; },
+});
 
 
 Zotero.defineProperty(Zotero.Item.prototype, 'firstCreator', {
@@ -1048,8 +1051,7 @@ Zotero.Item.prototype.setCreator = function (orderIndex, data) {
 		var msg = "Creator type '" + Zotero.CreatorTypes.getName(data.creatorTypeID) + "' "
 			+ "isn't valid for " + Zotero.ItemTypes.getName(itemTypeID)
 			+ " -- changing to primary creator";
-		Zotero.debug(msg, 2);
-		Components.utils.reportError(msg);
+		Zotero.warn(msg);
 		data.creatorTypeID = Zotero.CreatorTypes.getPrimaryIDForType(itemTypeID);
 	}
 	
@@ -1623,6 +1625,11 @@ Zotero.Item.prototype._saveData = Zotero.Promise.coroutine(function* (env) {
 		yield Zotero.DB.queryAsync(sql, [parentItemID, this.id]);
 	}
 	
+	// There's no reload for parentKey, so clear it here
+	if (this._changed.parentKey) {
+		this._clearChanged('parentKey');
+	}
+	
 	// Note
 	if ((isNew && this.isNote()) || this._changed.note) {
 		if (!isNew) {
@@ -1636,8 +1643,7 @@ Zotero.Item.prototype._saveData = Zotero.Promise.coroutine(function* (env) {
 		let noteText = this._noteText ? this._noteText : '';
 		// Add <div> wrapper if not present
 		if (!noteText.match(/^<div class="zotero-note znv[0-9]+">[\s\S]*<\/div>$/)) {
-			// Keep consistent with getNote()
-			noteText = '<div class="zotero-note znv1">' + noteText + '</div>';
+			noteText = Zotero.Notes.notePrefix + noteText + Zotero.Notes.noteSuffix;
 		}
 		
 		let params = [
@@ -2115,6 +2121,15 @@ Zotero.Item.prototype.numAttachments = function (includeTrashed) {
 }
 
 
+Zotero.Item.prototype.numNonHTMLFileAttachments = function () {
+	this._requireData('childItems');
+	return this.getAttachments()
+		.map(itemID => Zotero.Items.get(itemID))
+		.filter(item => item.isFileAttachment() && item.attachmentContentType != 'text/html')
+		.length;
+};
+
+
 Zotero.Item.prototype.getFile = function () {
 	Zotero.debug("Zotero.Item.prototype.getFile() is deprecated -- use getFilePath[Async]()", 2);
 	
@@ -2191,13 +2206,21 @@ Zotero.Item.prototype.getFilePath = function () {
 	//
 	// These should only exist if they weren't converted in the 80 DB upgrade step because
 	// the file couldn't be found.
-	if (Zotero.isMac && path.startsWith('AAAA')) {
+	if (path.startsWith('AAAA')) {
+		// These can only be resolved on Macs
+		if (!Zotero.isMac) {
+			Zotero.debug(`Can't resolve old-style attachment path '${path}' on non-Mac platform`);
+			this._updateAttachmentStates(false);
+			return false;
+		}
+		
 		let file = Components.classes["@mozilla.org/file/local;1"]
 			.createInstance(Components.interfaces.nsILocalFile);
 		try {
 			file.persistentDescriptor = path;
 		}
 		catch (e) {
+			Zotero.debug(`Can't resolve old-style attachment path '${path}'`);
 			this._updateAttachmentStates(false);
 			return false;
 		}
@@ -2205,7 +2228,7 @@ Zotero.Item.prototype.getFilePath = function () {
 		// If valid, convert this to a regular string in the background
 		Zotero.DB.queryAsync(
 			"UPDATE itemAttachments SET path=? WHERE itemID=?",
-			[file.leafName, this._id]
+			[file.path, this._id]
 		);
 		
 		return file.path;
@@ -2408,73 +2431,78 @@ Zotero.Item.prototype.fileExistsCached = function () {
 
 
 
-/*
+/**
  * Rename file associated with an attachment
  *
- * -1   		Destination file exists -- use _force_ to overwrite
- * -2		Error renaming
- * false		Attachment file not found
+ * @param {String} newName
+ * @param {Boolean} [overwrite=false] - Overwrite file if one exists
+ * @param {Boolean} [unique=false] - Add suffix to create unique filename if necessary
+ * @return {Number|false} -- true - Rename successful
+ *                           -1 - Destination file exists; use _force_ to overwrite
+ *                           -2 - Error renaming
+ *                           false - Attachment file not found
  */
-Zotero.Item.prototype.renameAttachmentFile = Zotero.Promise.coroutine(function* (newName, overwrite) {
-	var origPath = yield this.getFilePathAsync();
+Zotero.Item.prototype.renameAttachmentFile = async function (newName, overwrite = false, unique = false) {
+	var origPath = await this.getFilePathAsync();
 	if (!origPath) {
 		Zotero.debug("Attachment file not found in renameAttachmentFile()", 2);
 		return false;
 	}
 	
 	try {
-		var origName = OS.Path.basename(origPath);
-		var origModDate = (yield OS.File.stat(origPath)).lastModificationDate;
+		let origName = OS.Path.basename(origPath);
+		if (this.isImportedAttachment()) {
+			var origModDate = (await OS.File.stat(origPath)).lastModificationDate;
+		}
 		
-		newName = Zotero.File.getValidFileName(newName);
-		
-		// Ignore if no change
+		// No change
 		if (origName === newName) {
 			Zotero.debug("Filename has not changed");
 			return true;
 		}
 		
-		var destPath = OS.Path.join(OS.Path.dirname(origPath), newName);
-		var destName = OS.Path.basename(destPath);
-		
 		// Update mod time and clear hash so the file syncs
 		// TODO: use an integer counter instead of mod time for change detection
 		// Update mod time first, because it may fail for read-only files on Windows
-		yield OS.File.setDates(origPath, null, null);
-		var result = yield OS.File.move(origPath, destPath, { noOverwrite: !overwrite })
-		// If no overwriting and file exists, return -1
-		.catch(OS.File.Error, function (e) {
-			if (e.becauseExists) {
-				return -1;
-			}
-			throw e;
-		});
-		if (result) {
-			return result;
+		if (this.isImportedAttachment()) {
+			await OS.File.setDates(origPath, null, null);
 		}
 		
-		yield this.relinkAttachmentFile(destPath);
+		newName = await Zotero.File.rename(
+			origPath,
+			newName,
+			{
+				overwrite,
+				unique
+			}
+		);
+		let destPath = OS.Path.join(OS.Path.dirname(origPath), newName);
+		
+		await this.relinkAttachmentFile(destPath);
 		
 		if (this.isImportedAttachment()) {
 			this.attachmentSyncedHash = null;
 			this.attachmentSyncState = "to_upload";
-			yield this.saveTx({ skipAll: true });
+			await this.saveTx({ skipAll: true });
 		}
 		
 		return true;
 	}
 	catch (e) {
+		Zotero.logError(e);
+		
 		// Restore original modification date in case we managed to change it
-		try {
-			OS.File.setDates(origPath, null, origModDate);
-		} catch (e) {
-			Zotero.debug(e, 2);
+		if (this.isImportedAttachment()) {
+			try {
+				OS.File.setDates(origPath, null, origModDate);
+			} catch (e) {
+				Zotero.debug(e, 2);
+			}
 		}
-		Zotero.debug(e);
-		Components.utils.reportError(e);
+		
 		return -2;
 	}
-});
+};
 
 
 /**
@@ -2783,7 +2811,7 @@ Zotero.defineProperty(Zotero.Item.prototype, 'attachmentFilename', {
 		if (!path) {
 			return '';
 		}
-		var prefixedPath = path.match(/^(?:attachments|storage):(.+)$/);
+		var prefixedPath = path.match(/^(?:attachments|storage):(.*)$/);
 		if (prefixedPath) {
 			return prefixedPath[1];
 		}
@@ -3087,7 +3115,6 @@ Zotero.defineProperty(Zotero.Item.prototype, 'attachmentHash', {
  *
  * - Currently works on HTML, PDF and plaintext attachments
  * - Paragraph breaks will be lost in PDF content
- * - For PDFs, will return empty string if Zotero.Fulltext.pdfConverterIsRegistered() is false
  *
  * @return {Promise<String>} - A promise for attachment text or empty string if unavailable
  */
@@ -3141,10 +3168,6 @@ Zotero.defineProperty(Zotero.Item.prototype, 'attachmentText', {
 			}
 			
 			if (reindex) {
-				if (!Zotero.Fulltext.pdfConverterIsRegistered()) {
-					Zotero.debug("PDF converter is unavailable -- returning empty .attachmentText", 3);
-					return '';
-				}
 				yield Zotero.Fulltext.indexItems(this.id, false);
 			}
 			
@@ -3964,6 +3987,89 @@ Zotero.Item.prototype.clone = function (libraryID, options = {}) {
 }
 
 
+/**
+ * @param {Zotero.Item} item
+ * @param {Integer} libraryID
+ * @return {Zotero.Item} - New item
+ */
+Zotero.Item.prototype.moveToLibrary = async function (libraryID, onSkippedAttachment) {
+	if (!this.isEditable) {
+		throw new Error("Can't move item in read-only library");
+	}
+	var library = Zotero.Libraries.get(libraryID);
+	Zotero.debug("Moving item to " + library.name);
+	if (!library.editable) {
+		throw new Error("Can't move item to read-only library");
+	}
+	var filesEditable = library.filesEditable;
+	var allowsLinkedFiles = library.allowsLinkedFiles;
+	
+	var newItem = await Zotero.DB.executeTransaction(async function () {
+		// Create new clone item in target library
+		var newItem = this.clone(libraryID);
+		var newItemID = await newItem.save({
+			skipSelect: true
+		});
+		
+		if (this.isNote()) {
+			// Delete old item
+			await this.erase();
+			return newItem;
+		}
+		
+		// For regular items, add child items
+		
+		// Child notes
+		var noteIDs = this.getNotes();
+		var notes = Zotero.Items.get(noteIDs);
+		for (let note of notes) {
+			let newNote = note.clone(libraryID);
+			newNote.parentID = newItemID;
+			await newNote.save({
+				skipSelect: true
+			});
+		}
+		
+		// Child attachments
+		var attachmentIDs = this.getAttachments();
+		var attachments = Zotero.Items.get(attachmentIDs);
+		for (let attachment of attachments) {
+			let linkMode = attachment.attachmentLinkMode;
+			
+			// Skip linked files if not allowed in destination
+			if (!allowsLinkedFiles && linkMode == Zotero.Attachments.LINK_MODE_LINKED_FILE) {
+				Zotero.debug("Target library doesn't support linked files -- skipping attachment");
+				if (onSkippedAttachment) {
+					await onSkippedAttachment(attachment);
+				}
+				continue;
+			}
+			
+			// Skip files if not allowed in destination
+			if (!filesEditable && linkMode != Zotero.Attachments.LINK_MODE_LINKED_URL) {
+				Zotero.debug("Target library doesn't allow file editing -- skipping attachment");
+				if (onSkippedAttachment) {
+					await onSkippedAttachment(attachment);
+				}
+				continue;
+			}
+			
+			await Zotero.Attachments.moveAttachmentToLibrary(
+				attachment, libraryID, newItemID
+			);
+		}
+		
+		return newItem;
+	}.bind(this));
+	
+	// Delete old item. Do this outside of a transaction so we don't leave stranded files
+	// in the target library if deleting fails.
+	await this.eraseTx();
+	
+	return newItem;
+};
+
+
 Zotero.Item.prototype._eraseData = Zotero.Promise.coroutine(function* (env) {
 	Zotero.DB.requireTransaction();
 	
@@ -4088,6 +4194,9 @@ Zotero.Item.prototype.fromJSON = function (json) {
 		case 'mtime':
 		// Handled below
 		case 'collections':
+		case 'parentItem':
+		case 'deleted':
+		case 'inPublications':
 			break;
 		
 		case 'accessDate':
@@ -4116,15 +4225,6 @@ Zotero.Item.prototype.fromJSON = function (json) {
 			this[field] = val;
 			break;
 		
-		case 'parentItem':
-			this.parentKey = val;
-			break;
-		
-		case 'deleted':
-		case 'inPublications':
-			this[field] = !!val;
-			break;
-		
 		case 'creators':
 			this.setCreators(json.creators);
 			break;
@@ -4212,6 +4312,13 @@ Zotero.Item.prototype.fromJSON = function (json) {
 		let note = json.note;
 		this.setNote(note !== undefined ? note : "");
 	}
+	
+	// Update boolean fields that might not be present in JSON
+	['deleted', 'inPublications'].forEach(field => {
+		if (json[field] || this[field]) {
+			this[field] = !!json[field];
+		}
+	});
 }
 
 
@@ -4299,7 +4406,9 @@ Zotero.Item.prototype.toJSON = function (options = {}) {
 	}
 	
 	// My Publications
-	if (this._inPublications || mode == 'full') {
+	if (this._inPublications
+			// Include in 'full' mode, but only in My Library
+			|| (mode == 'full' && this.library && this.library.libraryType == 'user')) {
 		obj.inPublications = this._inPublications;
 	}
 	

chrome/content/zotero/xpcom/data/itemFields.js

@@ -260,6 +260,11 @@ Zotero.ItemFields = new function() {
 			throw new Error("Invalid field '" + baseField + '" for base field');
 		}
 		
+		// If field isn't a base field, return it if it's valid for the type
+		if (!this.isBaseField(baseFieldID)) {
+			return this.isValidForType(baseFieldID, itemTypeID) ? baseFieldID : false;
+		}
+		
 		return _baseTypeFields[itemTypeID][baseFieldID];
 	}
 	

chrome/content/zotero/xpcom/data/items.js

@@ -315,7 +315,21 @@ Zotero.Items = function() {
 			item._clearChanged('itemData');
 			
 			// Display titles
-			item.updateDisplayTitle()
+			try {
+				item.updateDisplayTitle()
+			}
+			catch (e) {
+				// A few item types need creators to be loaded. Instead of making
+				// updateDisplayTitle() async and loading conditionally, just catch the error
+				// and load on demand
+				if (e instanceof Zotero.Exception.UnloadedDataException) {
+					yield item.loadDataType('creators');
+					item.updateDisplayTitle()
+				}
+				else {
+					throw e;
+				}
+			}
 		}
 	});
 	
@@ -415,21 +429,31 @@ Zotero.Items = function() {
 					
 					// Convert non-HTML notes on-the-fly
 					if (note !== "") {
-						if (!note.substr(0, 36).match(/^<div class="zotero-note znv[0-9]+">/)) {
-							note = Zotero.Utilities.htmlSpecialChars(note);
-							note = Zotero.Notes.notePrefix + '<p>'
-								+ note.replace(/\n/g, '</p><p>')
-								.replace(/\t/g, '&nbsp;&nbsp;&nbsp;&nbsp;')
-								.replace(/  /g, '&nbsp;&nbsp;')
-								+ '</p>' + Zotero.Notes.noteSuffix;
-							note = note.replace(/<p>\s*<\/p>/g, '<p>&nbsp;</p>');
-							notesToUpdate.push([item.id, note]);
+						if (typeof note == 'number') {
+							note = '' + note;
+						}
+						if (typeof note == 'string') {
+							if (!note.substr(0, 36).match(/^<div class="zotero-note znv[0-9]+">/)) {
+								note = Zotero.Utilities.htmlSpecialChars(note);
+								note = Zotero.Notes.notePrefix + '<p>'
+									+ note.replace(/\n/g, '</p><p>')
+									.replace(/\t/g, '&nbsp;&nbsp;&nbsp;&nbsp;')
+									.replace(/  /g, '&nbsp;&nbsp;')
+									+ '</p>' + Zotero.Notes.noteSuffix;
+								note = note.replace(/<p>\s*<\/p>/g, '<p>&nbsp;</p>');
+								notesToUpdate.push([item.id, note]);
+							}
+							
+							// Don't include <div> wrapper when returning value
+							let startLen = note.substr(0, 36).match(/^<div class="zotero-note znv[0-9]+">/)[0].length;
+							let endLen = 6; // "</div>".length
+							note = note.substr(startLen, note.length - startLen - endLen);
+						}
+						// Clear null notes
+						else {
+							note = '';
+							notesToUpdate.push([item.id, '']);
 						}
-						
-						// Don't include <div> wrapper when returning value
-						let startLen = note.substr(0, 36).match(/^<div class="zotero-note znv[0-9]+">/)[0].length;
-						let endLen = 6; // "</div>".length
-						note = note.substr(startLen, note.length - startLen - endLen);
 					}
 					
 					item._noteText = note ? note : '';
@@ -725,6 +749,8 @@ Zotero.Items = function() {
 	
 	
 	this.merge = function (item, otherItems) {
+		Zotero.debug("Merging items");
+		
 		return Zotero.DB.executeTransaction(function* () {
 			var otherItemIDs = [];
 			var itemURI = Zotero.URI.getItemURI(item);
@@ -748,7 +774,10 @@ Zotero.Items = function() {
 				}
 				
 				// Add relations to master
-				item.setRelations(otherItem.getRelations());
+				let oldRelations = otherItem.getRelations();
+				for (let pred in oldRelations) {
+					oldRelations[pred].forEach(obj => item.addRelation(pred, obj));
+				}
 				
 				// Remove merge-tracking relations from other item, so that there aren't two
 				// subjects for a given deleted object
@@ -1176,6 +1205,25 @@ Zotero.Items = function() {
 	};
 	
 	
+	/**
+	 * Returns an array of items with children of selected parents removed
+	 *
+	 * @return {Zotero.Item[]}
+	 */
+	this.keepParents = function (items) {
+		var parentItems = new Set(
+			items
+				.filter(item => item.isTopLevelItem())
+				.map(item => item.id)
+		);
+		return items.filter(item => {
+			var parentItemID = item.parentItemID;
+			// Not a child item or not a child of one of the passed items
+			return !parentItemID || !parentItems.has(parentItemID);
+		});
+	}
+	
+	
 	/*
 	 * Generate SQL to retrieve firstCreator field
 	 *
@@ -1416,6 +1464,7 @@ Zotero.Items = function() {
 		return title.replace(/^[\[\'\"](.*)[\'\"\]]?$/, '$1')
 	}
 	
+	
 	Zotero.DataObjects.call(this);
 	
 	return this;

chrome/content/zotero/xpcom/data/library.js

@@ -190,6 +190,10 @@ Zotero.defineProperty(Zotero.Library.prototype, 'hasTrash', {
 	value: true
 });
 
+Zotero.defineProperty(Zotero.Library.prototype, 'allowsLinkedFiles', {
+	value: true
+});
+
 // Create other accessors
 (function() {
 	let accessors = ['editable', 'filesEditable', 'storageVersion', 'archived'];

chrome/content/zotero/xpcom/data/relations.js

@@ -32,7 +32,8 @@ Zotero.Relations = new function () {
 	
 	this._namespaces = {
 		dc: 'http://purl.org/dc/elements/1.1/',
-		owl: 'http://www.w3.org/2002/07/owl#'
+		owl: 'http://www.w3.org/2002/07/owl#',
+		mendeleyDB: 'http://zotero.org/namespaces/mendeleyDB#'
 	};
 	
 	var _types = ['collection', 'item'];
@@ -146,7 +147,7 @@ Zotero.Relations = new function () {
 	 * @return {Object[]} - An array of objects with a Zotero.DataObject as 'subject'
 	 *     and a predicate string as 'predicate'
 	 */
-	this.getByObject = function (objectType, object) {
+	this.getByObject = Zotero.Promise.coroutine(function* (objectType, object) {
 		var objectsClass = Zotero.DataObjectUtilities.getObjectsClassForObjectType(objectType);
 		var predicateIDs = [];
 		var o = _subjectPredicatesByObject[objectType]
@@ -156,13 +157,16 @@ Zotero.Relations = new function () {
 		}
 		var toReturn = [];
 		for (let predicateID in o) {
-			o[predicateID].forEach(subjectID => toReturn.push({
-				subject: objectsClass.get(subjectID),
-				predicate: Zotero.RelationPredicates.getName(predicateID)
-			}));
+			for (let subjectID of o[predicateID]) {
+				var subject = yield objectsClass.getAsync(subjectID);
+				toReturn.push({
+					subject: subject,
+					predicate: Zotero.RelationPredicates.getName(predicateID)
+				});
+			};
 		}
 		return toReturn;
-	};
+	});
 	
 	
 	this.updateUser = Zotero.Promise.coroutine(function* (fromUserID, toUserID) {
@@ -179,9 +183,9 @@ Zotero.Relations = new function () {
 			let objects = yield Zotero.DB.columnQueryAsync(
 				sql, 'http://zotero.org/users/' + fromUserID + '/%'
 			);
-			Zotero.DB.addCurrentCallback("commit", function () {
+			Zotero.DB.addCurrentCallback("commit", function* () {
 				for (let object of objects) {
-					let subPrefs = this.getByObject(type, object);
+					let subPrefs = yield this.getByObject(type, object);
 					let newObject = object.replace(
 						new RegExp("^http://zotero.org/users/" + fromUserID + "/(.*)"),
 						"http://zotero.org/users/" + toUserID + "/$1"
@@ -265,4 +269,4 @@ Zotero.Relations = new function () {
 		}
 		throw ("Invalid namespace in URI '" + uri + "' in Zotero.Relations._getPrefixAndValue()");
 	}
-}
+}

chrome/content/zotero/xpcom/data/searchConditions.js

@@ -338,7 +338,9 @@ Zotero.SearchConditions = new function(){
 					doesNotContain: true
 				},
 				table: 'itemNotes',
-				field: 'note'
+				// Exclude note prefix and suffix
+				field: `SUBSTR(note, ${1 + Zotero.Notes.notePrefix.length}, `
+					+ `LENGTH(note) - ${Zotero.Notes.notePrefix.length + Zotero.Notes.noteSuffix.length})`
 			},
 			
 			{
@@ -348,7 +350,9 @@ Zotero.SearchConditions = new function(){
 					doesNotContain: true
 				},
 				table: 'items',
-				field: 'note'
+				// Exclude note prefix and suffix
+				field: `SUBSTR(note, ${1 + Zotero.Notes.notePrefix.length}, `
+					+ `LENGTH(note) - ${Zotero.Notes.notePrefix.length + Zotero.Notes.noteSuffix.length})`
 			},
 			
 			{

chrome/content/zotero/xpcom/data/searches.js

@@ -96,6 +96,13 @@ Zotero.Searches = function() {
 	}
 	
 	
+	this.conditionEquals = function (data1, data2) {
+		return data1.condition === data2.condition
+			&& data1.operator === data2.operator
+			&& data1.value === data2.value;
+	},
+	
+	
 	this._loadConditions = Zotero.Promise.coroutine(function* (libraryID, ids, idSQL) {
 		var sql = "SELECT savedSearchID, searchConditionID, condition, operator, value, required "
 			+ "FROM savedSearches LEFT JOIN savedSearchConditions USING (savedSearchID) "

chrome/content/zotero/xpcom/data/tags.js

@@ -154,41 +154,20 @@ Zotero.Tags = new function() {
 	
 	
 	/**
-	 * Get all tags within the items of a Zotero.Search object
+	 * Get all tags within the items of a temporary table of search results
 	 *
-	 * @param {Zotero.Search} search
-	 * @param {Array} [types] Array of tag types to fetch
+	 * @param {String} tmpTable  Temporary table with items to use
+	 * @param {Array} [types]  Array of tag types to fetch
 	 * @return {Promise<Object>}  Promise for object with tag data in API JSON format, keyed by tagID
 	 */
-	this.getAllWithinSearch = Zotero.Promise.coroutine(function* (search, types) {
-		var ids = yield search.search();
-		return this.getAllWithinItemsList(ids, types);
-	});
-	
-	
-	this.getAllWithinItemsList = Zotero.Promise.coroutine(function* (ids, types) {
-		if (!Array.isArray(ids)) {
-			throw new Error("ids must be an array");
-		}
-		if (!ids.length) {
-			return [];
-		}
-		
-		var prefix = "SELECT DISTINCT name AS tag, type FROM itemTags "
+	this.getAllWithinSearchResults = Zotero.Promise.coroutine(function* (tmpTable, types) {
+		var sql = "SELECT DISTINCT name AS tag, type FROM itemTags "
 			+ "JOIN tags USING (tagID) WHERE itemID IN "
-			+ "(";
-		var suffix = ") ";
+			+ "(SELECT itemID FROM " + tmpTable + ") ";
 		if (types) {
-			suffix += "AND type IN (" + types.join() + ") ";
+			sql += "AND type IN (" + types.join() + ") ";
 		}
-		// Don't include ids in debug output
-		Zotero.DB.logQuery(`${prefix}[...${ids.length}]${suffix}`);
-		var rows = yield Zotero.DB.queryAsync(
-			prefix + ids.map(id => parseInt(id)).join(",") + suffix,
-			false,
-			{ debug: false }
-		);
-		
+		var rows = yield Zotero.DB.queryAsync(sql);
 		return rows.map((row) => this.cleanData(row));
 	});
 	
@@ -452,9 +431,11 @@ Zotero.Tags = new function() {
 		
 		Zotero.DB.requireTransaction();
 		
+		var sql;
+		
 		// Use given tags, as long as they're orphaned
 		if (tagIDs) {
-			let sql = "CREATE TEMPORARY TABLE tagDelete (tagID INT PRIMARY KEY)";
+			sql = "CREATE TEMPORARY TABLE tagDelete (tagID INT PRIMARY KEY)";
 			yield Zotero.DB.queryAsync(sql);
 			yield Zotero.Utilities.Internal.forEachChunkAsync(
 				tagIDs,
@@ -467,13 +448,17 @@ Zotero.Tags = new function() {
 					);
 				}
 			);
-			sql = "SELECT tagID AS id, name FROM tagDelete JOIN tags USING (tagID) "
-				+ "WHERE tagID NOT IN (SELECT tagID FROM itemTags)";
+			
+			// Skip tags that are still linked to items
+			sql = "DELETE FROM tagDelete WHERE tagID IN (SELECT tagID FROM itemTags)";
+			yield Zotero.DB.queryAsync(sql);
+			
+			sql = "SELECT tagID AS id, name FROM tagDelete JOIN tags USING (tagID)";
 			var toDelete = yield Zotero.DB.queryAsync(sql);
 		}
 		// Look for orphaned tags
 		else {
-			var sql = "CREATE TEMPORARY TABLE tagDelete AS "
+			sql = "CREATE TEMPORARY TABLE tagDelete AS "
 				+ "SELECT tagID FROM tags WHERE tagID NOT IN (SELECT tagID FROM itemTags)";
 			yield Zotero.DB.queryAsync(sql);
 			
@@ -482,11 +467,10 @@ Zotero.Tags = new function() {
 			
 			sql = "SELECT tagID AS id, name FROM tagDelete JOIN tags USING (tagID)";
 			var toDelete = yield Zotero.DB.queryAsync(sql);
-			
-			if (!toDelete.length) {
-				sql = "DROP TABLE tagDelete";
-				return Zotero.DB.queryAsync(sql);
-			}
+		}
+		
+		if (!toDelete.length) {
+			return Zotero.DB.queryAsync("DROP TABLE tagDelete");
 		}
 		
 		var ids = [];
@@ -774,12 +758,13 @@ Zotero.Tags = new function() {
 	 * @return {Q Promise} A Q promise for a data: URL for a PNG
 	 */
 	this.generateItemsListImage = function (colors, extraImage) {
-		var multiplier = (extraImage && extraImage.indexOf('2x') != -1) ? 2 : 1;
+		var multiplier = Zotero.hiDPI ? 2 : 1;
 		
 		var swatchWidth = 8 * multiplier;
 		var separator = 3 * multiplier;
 		var extraImageSeparator = 1 * multiplier;
 		var extraImageWidth = 16 * multiplier;
+		var extraImageHeight = 16 * multiplier;
 		var canvasHeight = 16 * multiplier;
 		var swatchHeight = 8 * multiplier;
 		var prependExtraImage = true;
@@ -847,7 +832,7 @@ Zotero.Tags = new function() {
 			
 			// When extra image has loaded, draw it
 			img.onload = function () {
-				ctx.drawImage(img, x, 0);
+				ctx.drawImage(img, x, 0, extraImageWidth, extraImageHeight);
 				
 				var dataURI = canvas.toDataURL("image/png");
 				var dataURIPromise = Zotero.Promise.resolve(dataURI);
@@ -868,7 +853,7 @@ Zotero.Tags = new function() {
 		// for the composite image once it's ready
 		return _itemsListExtraImagePromises[extraImage]
 		.then(function (img) {
-			ctx.drawImage(img, x, 0);
+			ctx.drawImage(img, x, 0, extraImageWidth, extraImageHeight);
 			
 			var dataURI = canvas.toDataURL("image/png");
 			var dataURIPromise = Zotero.Promise.resolve(dataURI);

chrome/content/zotero/xpcom/dataDirectory.js

@@ -178,8 +178,27 @@ Zotero.DataDirectory = {
 		// New installation of 5.0+ with no data directory specified, so check all the places the data
 		// could be
 		else {
+			Zotero.fxProfileAccessError = false;
+			
 			dataDir = this.defaultDir;
 			
+			// If there's already a profile pointing to the default location, use a different
+			// data directory named after the profile, as long as one either doesn't exist yet or
+			// one does and it contains a database
+			try {
+				if ((yield Zotero.Profile.findOtherProfilesUsingDataDirectory(dataDir, false)).length) {
+					let profileName = OS.Path.basename(Zotero.Profile.dir).match(/[^.]+\.(.+)/)[1];
+					let newDataDir = this.defaultDir + ' ' + profileName;
+					if (!(yield OS.File.exists(newDataDir))
+							|| (yield OS.File.exists(OS.Path.join(newDataDir, dbFilename)))) {
+						dataDir = newDataDir;
+					}
+				}
+			}
+			catch (e) {
+				Zotero.logError(e);
+			}
+			
 			// Check for ~/Zotero/zotero.sqlite
 			let dbFile = OS.Path.join(dataDir, dbFilename);
 			if (yield OS.File.exists(dbFile)) {
@@ -227,6 +246,7 @@ Zotero.DataDirectory = {
 				Zotero.debug("An error occurred locating the Firefox profile; "
 					+ "not attempting to migrate from Zotero for Firefox");
 				Zotero.logError(e);
+				Zotero.fxProfileAccessError = true;
 			}
 			if (defProfile) {
 				let profileDir = defProfile[0];
@@ -235,35 +255,7 @@ Zotero.DataDirectory = {
 				// Read in prefs
 				let prefsFile = OS.Path.join(profileDir, "prefs.js");
 				if (yield OS.File.exists(prefsFile)) {
-					// build sandbox
-					var sandbox = new Components.utils.Sandbox("http://www.example.com/");
-					Components.utils.evalInSandbox(
-						"var prefs = {};"+
-						"function user_pref(key, val) {"+
-							"prefs[key] = val;"+
-						"}"
-					, sandbox);
-					
-					(yield Zotero.File.getContentsAsync(prefsFile))
-						.split(/\n/)
-						.filter((line) => {
-							// Strip comments
-							return !line.startsWith('#')
-								// Only process lines in our pref branch
-								&& line.includes(ZOTERO_CONFIG.PREF_BRANCH);
-						})
-						// Process each line individually
-						.forEach((line) => {
-							try {
-								Zotero.debug("Processing " + line);
-								Components.utils.evalInSandbox(line, sandbox);
-							}
-							catch (e) {
-								Zotero.logError("Error processing prefs line: " + line);
-							}
-						});
-					
-					var prefs = sandbox.prefs;
+					let prefs = yield Zotero.Profile.readPrefsFromFile(prefsFile);
 					
 					// Check for data dir pref
 					if (prefs['extensions.zotero.dataDir'] && prefs['extensions.zotero.useDataDir']) {
@@ -304,6 +296,7 @@ Zotero.DataDirectory = {
 								e.dataDir = nsIFile.path;
 								throw e;
 							}
+							Zotero.fxProfileAccessError = true;
 						}
 					}
 					// If no custom dir specified, check for a subdirectory
@@ -325,6 +318,7 @@ Zotero.DataDirectory = {
 						catch (e) {
 							if (!(e instanceof OS.File.Error && e.becauseNoSuchFile)) {
 								Zotero.logError(e);
+								Zotero.fxProfileAccessError = true;
 							}
 						}
 					}
@@ -716,7 +710,7 @@ Zotero.DataDirectory = {
 			let dontAskAgain = {};
 			let index = ps.confirmEx(null,
 				"Other Data Directory Found",
-				"Zotero found a previous data directory within your Firefox profile directory, "
+				"Zotero found a previous data directory within your Firefox profile, "
 					+ `last modified on ${mtime.toLocaleDateString()}. `
 					+ "If items or files are missing from Zotero that were present in Zotero for Firefox, "
 					+ "your previous data directory may not have been properly migrated to the new default location "
@@ -835,14 +829,21 @@ Zotero.DataDirectory = {
 		}
 		
 		// Skip migration if new dir on different drive and prompt
-		if (yield this.isNewDirOnDifferentDrive(dataDir, newDir)) {
-			Zotero.debug(`New dataDir ${newDir} is on a different drive from ${dataDir} -- skipping migration`);
-			Zotero.DataDirectory.newDirOnDifferentDrive = true;
-			
-			let error = Zotero.getString(`dataDir.migration.failure.full.automatic.newDirOnDifferentDrive`, Zotero.clientName)
-				+ "\n\n"
-				+ Zotero.getString(`dataDir.migration.failure.full.automatic.text2`, Zotero.appName);
-			return this.fullMigrationFailurePrompt(dataDir, newDir, error);
+		try {
+			if (yield this.isNewDirOnDifferentDrive(dataDir, newDir)) {
+				Zotero.debug(`New dataDir ${newDir} is on a different drive from ${dataDir} -- skipping migration`);
+				Zotero.DataDirectory.newDirOnDifferentDrive = true;
+				
+				let error = Zotero.getString(`dataDir.migration.failure.full.automatic.newDirOnDifferentDrive`, Zotero.clientName)
+					+ "\n\n"
+					+ Zotero.getString(`dataDir.migration.failure.full.automatic.text2`, Zotero.appName);
+				return this.fullMigrationFailurePrompt(dataDir, newDir, error);
+			}
+		}
+		catch (e) {
+			Zotero.logError("Error checking whether data directory is on different drive "
+				+ "-- skipping migration:\n\n" + e);
+			return false;
 		}
 		
 		// Check for an existing pipe from other running versions of Zotero pointing at the same data

chrome/content/zotero/xpcom/date.js

@@ -296,13 +296,13 @@ Zotero.Date = new function(){
 		
 		// Parse 'yesterday'/'today'/'tomorrow'
 		var lc = (string + '').toLowerCase();
-		if (lc == 'yesterday' || (Zotero.getString && lc === Zotero.getString('date.yesterday'))) {
+		if (lc == 'yesterday' || (Zotero.isClient && lc === Zotero.getString('date.yesterday'))) {
 			string = Zotero.Date.dateToSQL(new Date(Date.now() - 1000*60*60*24)).substr(0, 10); // no 'this' for translator sandbox
 		}
-		else if (lc == 'today' || (Zotero.getString && lc == Zotero.getString('date.today'))) {
+		else if (lc == 'today' || (Zotero.isClient && lc == Zotero.getString('date.today'))) {
 			string = Zotero.Date.dateToSQL(new Date()).substr(0, 10);
 		}
-		else if (lc == 'tomorrow' || (Zotero.getString && lc == Zotero.getString('date.tomorrow'))) {
+		else if (lc == 'tomorrow' || (Zotero.isClient && lc == Zotero.getString('date.tomorrow'))) {
 			string = Zotero.Date.dateToSQL(new Date(Date.now() + 1000*60*60*24)).substr(0, 10);
 		}
 		else {

chrome/content/zotero/xpcom/db.js

@@ -31,8 +31,8 @@
 // the same database is accessed simultaneously by multiple Zotero instances.
 const DB_LOCK_EXCLUSIVE = true;
 
-Zotero.DBConnection = function(dbName) {
-	if (!dbName) {
+Zotero.DBConnection = function(dbNameOrPath) {
+	if (!dbNameOrPath) {
 		throw ('DB name not provided in Zotero.DBConnection()');
 	}
 	
@@ -70,8 +70,18 @@ Zotero.DBConnection = function(dbName) {
 		return Zotero.Date.toUnixTimestamp(d);
 	});
 	
-	// Private members
-	this._dbName = dbName;
+	// Absolute path to DB
+	if (dbNameOrPath.startsWith('/') || (Zotero.isWin && dbNameOrPath.includes('\\'))) {
+		this._dbName = OS.Path.basename(dbNameOrPath).replace(/\.sqlite$/, '');
+		this._dbPath = dbNameOrPath;
+		this._externalDB = true;
+	}
+	// DB name in data directory
+	else {
+		this._dbName = dbNameOrPath;
+		this._dbPath = Zotero.DataDirectory.getDatabase(dbNameOrPath);
+		this._externalDB = false;
+	}
 	this._shutdown = false;
 	this._connection = null;
 	this._transactionID = null;
@@ -91,6 +101,14 @@ Zotero.DBConnection = function(dbName) {
 	this._dbIsCorrupt = null
 	
 	this._transactionPromise = null;
+	
+	if (dbNameOrPath == 'zotero') {
+		this.IncompatibleVersionException = function (msg, dbClientVersion) {
+			this.message = msg;
+			this.dbClientVersion = dbClientVersion;
+		}
+		this.IncompatibleVersionException.prototype = Object.create(Error.prototype);
+	}
 }
 
 /////////////////////////////////////////////////////////////////
@@ -105,7 +123,7 @@ Zotero.DBConnection = function(dbName) {
  * @return	void
  */
 Zotero.DBConnection.prototype.test = function () {
-	return this._getConnectionAsync().return();
+	return this._getConnectionAsync().then(() => {});
 }
 
 Zotero.DBConnection.prototype.getAsyncStatement = Zotero.Promise.coroutine(function* (sql) {
@@ -485,7 +503,7 @@ Zotero.DBConnection.prototype.executeTransaction = Zotero.Promise.coroutine(func
 		// Run begin callbacks
 		for (var i=0; i<this._callbacks.begin.length; i++) {
 			if (this._callbacks.begin[i]) {
-				this._callbacks.begin[i]();
+				this._callbacks.begin[i](id);
 			}
 		}
 		var conn = this._getConnection(options) || (yield this._getConnectionAsync(options));
@@ -516,13 +534,13 @@ Zotero.DBConnection.prototype.executeTransaction = Zotero.Promise.coroutine(func
 		// Run temporary commit callbacks
 		var f;
 		while (f = this._callbacks.current.commit.shift()) {
-			yield Zotero.Promise.resolve(f());
+			yield Zotero.Promise.resolve(f(id));
 		}
 		
 		// Run commit callbacks
 		for (var i=0; i<this._callbacks.commit.length; i++) {
 			if (this._callbacks.commit[i]) {
-				yield this._callbacks.commit[i]();
+				yield this._callbacks.commit[i](id);
 			}
 		}
 		
@@ -549,13 +567,13 @@ Zotero.DBConnection.prototype.executeTransaction = Zotero.Promise.coroutine(func
 		// Run temporary commit callbacks
 		var f;
 		while (f = this._callbacks.current.rollback.shift()) {
-			yield Zotero.Promise.resolve(f());
+			yield Zotero.Promise.resolve(f(id));
 		}
 		
 		// Run rollback callbacks
 		for (var i=0; i<this._callbacks.rollback.length; i++) {
 			if (this._callbacks.rollback[i]) {
-				yield Zotero.Promise.resolve(this._callbacks.rollback[i]());
+				yield Zotero.Promise.resolve(this._callbacks.rollback[i](id));
 			}
 		}
 		
@@ -818,9 +836,10 @@ Zotero.DBConnection.prototype.logQuery = function (sql, params = [], options) {
 }
 
 
-Zotero.DBConnection.prototype.tableExists = Zotero.Promise.coroutine(function* (table) {
+Zotero.DBConnection.prototype.tableExists = Zotero.Promise.coroutine(function* (table, db) {
 	yield this._getConnectionAsync();
-	var sql = "SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND tbl_name=?";
+	var prefix = db ? db + '.' : '';
+	var sql = `SELECT COUNT(*) FROM ${prefix}sqlite_master WHERE type='table' AND tbl_name=?`;
 	var count = yield this.valueQueryAsync(sql, [table]);
 	return !!count;
 });
@@ -879,7 +898,7 @@ Zotero.DBConnection.prototype.vacuum = function () {
 // TEMP
 Zotero.DBConnection.prototype.info = Zotero.Promise.coroutine(function* () {
 	var info = {};
-	var pragmas = ['auto_vacuum', 'cache_size', 'locking_mode', 'page_size'];
+	var pragmas = ['auto_vacuum', 'cache_size', 'main.locking_mode', 'page_size'];
 	for (let p of pragmas) {
 		info[p] = yield Zotero.DB.valueQueryAsync(`PRAGMA ${p}`);
 	}
@@ -894,9 +913,13 @@ Zotero.DBConnection.prototype.integrityCheck = Zotero.Promise.coroutine(function
 
 
 Zotero.DBConnection.prototype.checkException = function (e) {
+	if (this._externalDB) {
+		return true;
+	}
+	
 	if (e.message.includes(this.DB_CORRUPTION_STRING)) {
 		// Write corrupt marker to data directory
-		var file = Zotero.File.pathToFile(Zotero.DataDirectory.getDatabase(this._dbName, 'is.corrupt'));
+		var file = Zotero.File.pathToFile(this._dbPath + '.is.corrupt');
 		Zotero.File.putContents(file, '');
 		
 		this._dbIsCorrupt = true;
@@ -947,6 +970,11 @@ Zotero.DBConnection.prototype.closeDatabase = Zotero.Promise.coroutine(function*
 
 
 Zotero.DBConnection.prototype.backupDatabase = Zotero.Promise.coroutine(function* (suffix, force) {
+	if (this.skipBackup || this._externalDB || Zotero.skipLoading) {
+		this._debug("Skipping backup of database '" + this._dbName + "'", 1);
+		return false;
+	}
+	
 	var storageService = Components.classes["@mozilla.org/storage/service;1"]
 		.getService(Components.interfaces.mozIStorageService);
 	
@@ -980,27 +1008,21 @@ Zotero.DBConnection.prototype.backupDatabase = Zotero.Promise.coroutine(function
 	});
 	
 	try {
-		var corruptMarker = Zotero.File.pathToFile(
-			Zotero.DataDirectory.getDatabase(this._dbName, 'is.corrupt')
-		);
+		let corruptMarker = Zotero.File.pathToFile(this._dbPath + '.is.corrupt');
 		
-		if (this.skipBackup || Zotero.skipLoading) {
-			this._debug("Skipping backup of database '" + this._dbName + "'", 1);
-			return false;
-		}
-		else if (this._dbIsCorrupt || corruptMarker.exists()) {
+		if (this._dbIsCorrupt || corruptMarker.exists()) {
 			this._debug("Database '" + this._dbName + "' is marked as corrupt -- skipping backup", 1);
 			return false;
 		}
 		
-		var file = Zotero.File.pathToFile(Zotero.DataDirectory.getDatabase(this._dbName));
+		let file = this._dbPath;
 		
 		// For standard backup, make sure last backup is old enough to replace
 		if (!suffix && !force) {
-			var backupFile = Zotero.File.pathToFile(Zotero.DataDirectory.getDatabase(this._dbName, 'bak'));
-			if (yield OS.File.exists(backupFile.path)) {
-				var currentDBTime = (yield OS.File.stat(file.path)).lastModificationDate;
-				var lastBackupTime = (yield OS.File.stat(backupFile.path)).lastModificationDate;
+			let backupFile = this._dbPath + '.bak';
+			if (yield OS.File.exists(backupFile)) {
+				let currentDBTime = (yield OS.File.stat(file.path)).lastModificationDate;
+				let lastBackupTime = (yield OS.File.stat(backupFile)).lastModificationDate;
 				if (currentDBTime == lastBackupTime) {
 					Zotero.debug("Database '" + this._dbName + "' hasn't changed -- skipping backup");
 					return;
@@ -1021,7 +1043,7 @@ Zotero.DBConnection.prototype.backupDatabase = Zotero.Promise.coroutine(function
 		
 		// Copy via a temporary file so we don't run into disk space issues
 		// after deleting the old backup file
-		var tmpFile = Zotero.DataDirectory.getDatabase(this._dbName, 'tmp');
+		var tmpFile = this._dbPath + '.tmp';
 		if (yield OS.File.exists(tmpFile)) {
 			try {
 				yield OS.File.remove(tmpFile);
@@ -1038,18 +1060,21 @@ Zotero.DBConnection.prototype.backupDatabase = Zotero.Promise.coroutine(function
 		// the lock is lost
 		try {
 			if (DB_LOCK_EXCLUSIVE) {
-				yield this.queryAsync("PRAGMA locking_mode=NORMAL", false, { inBackup: true });
+				yield this.queryAsync("PRAGMA main.locking_mode=NORMAL", false, { inBackup: true });
 			}
-			storageService.backupDatabaseFile(file, OS.Path.basename(tmpFile), file.parent);
+			storageService.backupDatabaseFile(
+				Zotero.File.pathToFile(file),
+				OS.Path.basename(tmpFile),
+				Zotero.File.pathToFile(file).parent
+			);
 		}
 		catch (e) {
-			Zotero.debug(e);
-			Components.utils.reportError(e);
+			Zotero.logError(e);
 			return false;
 		}
 		finally {
 			if (DB_LOCK_EXCLUSIVE) {
-				yield this.queryAsync("PRAGMA locking_mode=EXCLUSIVE", false, { inBackup: true });
+				yield this.queryAsync("PRAGMA main.locking_mode=EXCLUSIVE", false, { inBackup: true });
 			}
 		}
 		
@@ -1080,7 +1105,7 @@ Zotero.DBConnection.prototype.backupDatabase = Zotero.Promise.coroutine(function
 		// Special backup
 		if (!suffix && numBackups > 1) {
 			// Remove oldest backup file
-			var targetFile = Zotero.DataDirectory.getDatabase(this._dbName, (numBackups - 1) + '.bak');
+			let targetFile = this._dbPath + '.' + (numBackups - 1) + '.bak';
 			if (yield OS.File.exists(targetFile)) {
 				yield OS.File.remove(targetFile);
 			}
@@ -1090,12 +1115,8 @@ Zotero.DBConnection.prototype.backupDatabase = Zotero.Promise.coroutine(function
 				var targetNum = i;
 				var sourceNum = targetNum - 1;
 				
-				var targetFile = Zotero.DataDirectory.getDatabase(
-					this._dbName, targetNum + '.bak'
-				);
-				var sourceFile = Zotero.DataDirectory.getDatabase(
-					this._dbName, sourceNum ? sourceNum + '.bak' : 'bak'
-				);
+				let targetFile = this._dbPath + '.' + targetNum + '.bak';
+				let sourceFile = this._dbPath + '.' + (sourceNum ? sourceNum + '.bak' : 'bak')
 				
 				if (!(yield OS.File.exists(sourceFile))) {
 					continue;
@@ -1107,9 +1128,7 @@ Zotero.DBConnection.prototype.backupDatabase = Zotero.Promise.coroutine(function
 			}
 		}
 		
-		var backupFile = Zotero.DataDirectory.getDatabase(
-			this._dbName, (suffix ? suffix + '.' : '') + 'bak'
-		);
+		let backupFile = this._dbPath + '.' + (suffix ? suffix + '.' : '') + 'bak';
 		
 		// Remove old backup file
 		if (yield OS.File.exists(backupFile)) {
@@ -1146,11 +1165,11 @@ Zotero.DBConnection.prototype._getConnection = function (options) {
 /*
  * Retrieve a link to the data store asynchronously
  */
-Zotero.DBConnection.prototype._getConnectionAsync = Zotero.Promise.coroutine(function* (options) {
+Zotero.DBConnection.prototype._getConnectionAsync = async function (options) {
 	// If a backup is in progress, wait until it's done
 	if (this._backupPromise && this._backupPromise.isPending() && (!options || !options.inBackup)) {
 		Zotero.debug("Waiting for database backup to complete", 2);
-		yield this._backupPromise;
+		await this._backupPromise;
 	}
 	
 	if (this._connection) {
@@ -1161,48 +1180,50 @@ Zotero.DBConnection.prototype._getConnectionAsync = Zotero.Promise.coroutine(fun
 	}
 	
 	this._debug("Asynchronously opening database '" + this._dbName + "'");
+	Zotero.debug(this._dbPath);
 	
 	// Get the storage service
 	var store = Components.classes["@mozilla.org/storage/service;1"].
 		getService(Components.interfaces.mozIStorageService);
 	
-	var file = Zotero.File.pathToFile(Zotero.DataDirectory.getDatabase(this._dbName));
-	var backupFile = Zotero.File.pathToFile(Zotero.DataDirectory.getDatabase(this._dbName, 'bak'));
-	
-	var fileName = this._dbName + '.sqlite';
+	var file = this._dbPath;
+	var backupFile = this._dbPath + '.bak';
+	var fileName = OS.Path.basename(file);
+	var corruptMarker = this._dbPath + '.is.corrupt';
 	
 	catchBlock: try {
-		var corruptMarker = Zotero.File.pathToFile(Zotero.DataDirectory.getDatabase(this._dbName, 'is.corrupt'));
-		if (corruptMarker.exists()) {
+		if (await OS.File.exists(corruptMarker)) {
 			throw new Error(this.DB_CORRUPTION_STRING);
 		}
-		this._connection = yield Zotero.Promise.resolve(this.Sqlite.openConnection({
-			path: file.path
+		this._connection = await Zotero.Promise.resolve(this.Sqlite.openConnection({
+			path: file
 		}));
 	}
 	catch (e) {
+		// Don't deal with corrupted external dbs
+		if (this._externalDB) {
+			throw e;
+		}
+		
 		Zotero.logError(e);
 		
 		if (e.message.includes(this.DB_CORRUPTION_STRING)) {
-			this._debug("Database file '" + file.leafName + "' corrupted", 1);
+			this._debug(`Database file '${fileName}' corrupted`, 1);
 			
 			// No backup file! Eek!
-			if (!backupFile.exists()) {
+			if (!await OS.File.exists(backupFile)) {
 				this._debug("No backup file for DB '" + this._dbName + "' exists", 1);
 				
 				// Save damaged filed
 				this._debug('Saving damaged DB file with .damaged extension', 1);
-				var damagedFile = Zotero.File.pathToFile(
-					Zotero.DataDirectory.getDatabase(this._dbName, 'damaged')
-				);
+				let damagedFile = this._dbPath + '.damaged';
 				Zotero.moveToUnique(file, damagedFile);
 				
 				// Create new main database
-				var file = Zotero.File.pathToFile(Zotero.DataDirectory.getDatabase(this._dbName));
 				this._connection = store.openDatabase(file);
 				
-				if (corruptMarker.exists()) {
-					corruptMarker.remove(null);
+				if (await OS.File.exists(corruptMarker)) {
+					await OS.File.remove(corruptMarker);
 				}
 				
 				Zotero.alert(
@@ -1215,24 +1236,21 @@ Zotero.DBConnection.prototype._getConnectionAsync = Zotero.Promise.coroutine(fun
 			
 			// Save damaged file
 			this._debug('Saving damaged DB file with .damaged extension', 1);
-			var damagedFile = Zotero.File.pathToFile(
-				Zotero.DataDirectory.getDatabase(this._dbName, 'damaged')
-			);
+			let damagedFile = this._dbPath + '.damaged';
 			Zotero.moveToUnique(file, damagedFile);
 			
 			// Test the backup file
 			try {
 				Zotero.debug("Asynchronously opening DB connection");
-				this._connection = yield Zotero.Promise.resolve(this.Sqlite.openConnection({
-					path: backupFile.path
+				this._connection = await Zotero.Promise.resolve(this.Sqlite.openConnection({
+					path: backupFile
 				}));
 			}
 			// Can't open backup either
 			catch (e) {
 				// Create new main database
-				var file = Zotero.File.pathToFile(Zotero.DataDirectory.getDatabase(this._dbName));
-				this._connection = yield Zotero.Promise.resolve(this.Sqlite.openConnection({
-					path: file.path
+				this._connection = await Zotero.Promise.resolve(this.Sqlite.openConnection({
+					path: file
 				}));
 				
 				Zotero.alert(
@@ -1241,8 +1259,8 @@ Zotero.DBConnection.prototype._getConnectionAsync = Zotero.Promise.coroutine(fun
 					Zotero.getString('db.dbRestoreFailed', fileName)
 				);
 				
-				if (corruptMarker.exists()) {
-					corruptMarker.remove(null);
+				if (await OS.File.exists(corruptMarker)) {
+					await OS.File.remove(corruptMarker);
 				}
 				
 				break catchBlock;
@@ -1253,7 +1271,7 @@ Zotero.DBConnection.prototype._getConnectionAsync = Zotero.Promise.coroutine(fun
 			// Copy backup file to main DB file
 			this._debug("Restoring database '" + this._dbName + "' from backup file", 1);
 			try {
-				backupFile.copyTo(backupFile.parent, fileName);
+				await OS.File.copy(backupFile, file);
 			}
 			catch (e) {
 				// TODO: deal with low disk space
@@ -1261,8 +1279,7 @@ Zotero.DBConnection.prototype._getConnectionAsync = Zotero.Promise.coroutine(fun
 			}
 			
 			// Open restored database
-			var file = OS.Path.join(Zotero.DataDirectory.dir, fileName);
-			this._connection = yield Zotero.Promise.resolve(this.Sqlite.openConnection({
+			this._connection = await Zotero.Promise.resolve(this.Sqlite.openConnection({
 				path: file
 			}));
 			this._debug('Database restored', 1);
@@ -1271,13 +1288,13 @@ Zotero.DBConnection.prototype._getConnectionAsync = Zotero.Promise.coroutine(fun
 				Zotero.getString('general.warning'),
 				Zotero.getString('db.dbRestored', [
 					fileName,
-					Zotero.Date.getFileDateString(backupFile),
-					Zotero.Date.getFileTimeString(backupFile)
+					Zotero.Date.getFileDateString(Zotero.File.pathToFile(backupFile)),
+					Zotero.Date.getFileTimeString(Zotero.File.pathToFile(backupFile))
 				])
 			);
 			
-			if (corruptMarker.exists()) {
-				corruptMarker.remove(null);
+			if (await OS.File.exists(corruptMarker)) {
+				await OS.File.remove(corruptMarker);
 			}
 			
 			break catchBlock;
@@ -1287,44 +1304,36 @@ Zotero.DBConnection.prototype._getConnectionAsync = Zotero.Promise.coroutine(fun
 		throw (e);
 	}
 	
-	if (DB_LOCK_EXCLUSIVE) {
-		yield this.queryAsync("PRAGMA locking_mode=EXCLUSIVE");
+	if (!this._externalDB) {
+		if (DB_LOCK_EXCLUSIVE) {
+			await this.queryAsync("PRAGMA main.locking_mode=EXCLUSIVE");
+		}
+		else {
+			await this.queryAsync("PRAGMA main.locking_mode=NORMAL");
+		}
+		
+		// Set page cache size to 8MB
+		let pageSize = await this.valueQueryAsync("PRAGMA page_size");
+		let cacheSize = 8192000 / pageSize;
+		await this.queryAsync("PRAGMA cache_size=" + cacheSize);
+		
+		// Enable foreign key checks
+		await this.queryAsync("PRAGMA foreign_keys=true");
+		
+		// Register idle observer for DB backup
+		Zotero.Schema.schemaUpdatePromise.then(() => {
+			Zotero.debug("Initializing DB backup idle observer");
+			var idleService = Components.classes["@mozilla.org/widget/idleservice;1"]
+				.getService(Components.interfaces.nsIIdleService);
+			idleService.addIdleObserver(this, 300);
+		});
 	}
-	else {
-		yield this.queryAsync("PRAGMA locking_mode=NORMAL");
-	}
-	
-	// Set page cache size to 8MB
-	var pageSize = yield this.valueQueryAsync("PRAGMA page_size");
-	var cacheSize = 8192000 / pageSize;
-	yield this.queryAsync("PRAGMA cache_size=" + cacheSize);
-	
-	// Enable foreign key checks
-	yield this.queryAsync("PRAGMA foreign_keys=true");
-	
-	// Register idle observer for DB backup
-	Zotero.Schema.schemaUpdatePromise.then(() => {
-		Zotero.debug("Initializing DB backup idle observer");
-		var idleService = Components.classes["@mozilla.org/widget/idleservice;1"]
-			.getService(Components.interfaces.nsIIdleService);
-		idleService.addIdleObserver(this, 300);
-	});
 	
 	return this._connection;
-});
+};
 
 
 Zotero.DBConnection.prototype._debug = function (str, level) {
 	var prefix = this._dbName == 'zotero' ? '' : '[' + this._dbName + '] ';
 	Zotero.debug(prefix + str, level);
 }
-
-
-// Initialize main database connection
-Zotero.DB = new Zotero.DBConnection('zotero');
-
-Zotero.DB.IncompatibleVersionException = function (msg, dbClientVersion) {
-	this.message = msg;
-	this.dbClientVersion = dbClientVersion;
-}
-Zotero.DB.IncompatibleVersionException.prototype = Object.create(Error.prototype);

chrome/content/zotero/xpcom/debug.js

@@ -139,7 +139,7 @@ Zotero.Debug = new function () {
 		}
 		
 		if (stack) {
-			message += '\n' + Zotero.Debug.stackToString(stack);
+			message += '\n' + this.stackToString(stack);
 		}
 		
 		if (_console || _consoleViewer) {
@@ -288,7 +288,7 @@ Zotero.Debug = new function () {
 				+ ':' + stack.lineNumber;
 			stack = stack.caller;
 		}
-		return str.substr(1);
+		return this.filterStack(str).substr(1);
 	};
 	
 	

chrome/content/zotero/xpcom/feedReader.js

@@ -407,9 +407,12 @@ Zotero.FeedReader._getFeedItem = function(feedEntry, feedInfo) {
 	
 	let date = Zotero.FeedReader._getFeedField(feedEntry, 'publicationDate', 'prism')
 		|| Zotero.FeedReader._getFeedField(feedEntry, 'date', 'dc')
+		// DEBUG: Why not get these from the feedEntry?
 		|| Zotero.FeedReader._getFeedField(feedEntry, 'pubDate') // RSS
-		|| Zotero.FeedReader._getFeedField(feedEntry, 'published') // Atom
-		|| Zotero.FeedReader._getFeedField(feedEntry, 'updated'); // Atom
+		|| Zotero.FeedReader._getFeedField(feedEntry, 'updated', 'atom') // Atom
+		|| Zotero.FeedReader._getFeedField(feedEntry, 'published', 'atom'); // Atom
+		
+	
 	if (date) item.date = date;
 	
 	let publicationTitle = Zotero.FeedReader._getFeedField(feedEntry, 'publicationName', 'prism')

chrome/content/zotero/xpcom/file.js

@@ -427,6 +427,82 @@ Zotero.File = new function(){
 	});
 	
 	
+	/**
+	 * Rename file within its parent directory
+	 *
+	 * @param {String} file - File path
+	 * @param {String} newName
+	 * @param {Object} [options]
+	 * @param {Boolean} [options.overwrite=false] - Overwrite file if one exists
+	 * @param {Boolean} [options.unique=false] - Add suffix to create unique filename if necessary
+	 * @return {String|false} - New filename, or false if destination file exists and `overwrite` not set
+	 */
+	this.rename = async function (file, newName, options = {}) {
+		var overwrite = options.overwrite || false;
+		var unique = options.unique || false;
+		
+		var origPath = file;
+		var origName = OS.Path.basename(origPath);
+		newName = Zotero.File.getValidFileName(newName);
+		
+		// Ignore if no change
+		if (origName === newName) {
+			Zotero.debug("Filename has not changed");
+			return origName;
+		}
+		
+		var parentDir = OS.Path.dirname(origPath);
+		var destPath = OS.Path.join(parentDir, newName);
+		var destName = OS.Path.basename(destPath);
+		// Get root + extension, if there is one
+		var pos = destName.lastIndexOf('.');
+		if (pos > 0) {
+			var root = destName.substr(0, pos);
+			var ext = destName.substr(pos + 1);
+		}
+		else {
+			var root = destName;
+		}
+		
+		var incr = 0;
+		while (true) {
+			// If filename already exists, add a numeric suffix to the end of the root, before
+			// the extension if there is one
+			if (incr) {
+				if (ext) {
+					destName = root + ' ' + (incr + 1) + '.' + ext;
+				}
+				else {
+					destName = root + ' ' + (incr + 1);
+				}
+				destPath = OS.Path.join(parentDir, destName);
+			}
+			
+			try {
+				Zotero.debug(`Renaming ${origPath} to ${OS.Path.basename(destPath)}`);
+				Zotero.debug(destPath);
+				await OS.File.move(origPath, destPath, { noOverwrite: !overwrite })
+			}
+			catch (e) {
+				if (e instanceof OS.File.Error) {
+					if (e.becauseExists) {
+						// Increment number to create unique suffix
+						if (unique) {
+							incr++;
+							continue;
+						}
+						// No overwriting or making unique and file exists
+						return false;
+					}
+				}
+				throw e;
+			}
+			break;
+		}
+		return destName;
+	};
+	
+	
 	/**
 	 * Delete a file if it exists, asynchronously
 	 *
@@ -690,6 +766,21 @@ Zotero.File = new function(){
 	}
 	
 	
+	this.setNormalFilePermissions = function (file) {
+		return OS.File.setPermissions(
+			file,
+			{
+				unixMode: 0o644,
+				winAttributes: {
+					readOnly: false,
+					hidden: false,
+					system: false
+				}
+			}
+		);
+	}
+	
+	
 	this.createShortened = function (file, type, mode, maxBytes) {
 		file = this.pathToFile(file);
 		

chrome/content/zotero/xpcom/fulltext.js

@@ -24,17 +24,8 @@
 */
 
 Zotero.Fulltext = Zotero.FullText = new function(){
-	const CACHE_FILE = '.zotero-ft-cache';
-	
-	this.pdfConverterIsRegistered = pdfConverterIsRegistered;
-	this.pdfInfoIsRegistered = pdfInfoIsRegistered;
 	this.isCachedMIMEType = isCachedMIMEType;
 	
-	this.pdfToolsDownloadBaseURL = ZOTERO_CONFIG.PDF_TOOLS_URL;
-	this.__defineGetter__("pdfToolsName", function() { return 'Xpdf'; });
-	this.__defineGetter__("pdfToolsURL", function() { return 'http://www.foolabs.com/xpdf/'; });
-	this.__defineGetter__("pdfConverterName", function() { return 'pdftotext'; });
-	this.__defineGetter__("pdfInfoName", function() { return 'pdfinfo'; });
 	this.__defineGetter__("pdfConverterCacheFile", function () { return '.zotero-ft-cache'; });
 	this.__defineGetter__("pdfInfoCacheFile", function () { return '.zotero-ft-info'; });
 	
@@ -60,16 +51,10 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 	const kWbClassHiraganaLetter =   5;
 	const kWbClassHWKatakanaLetter = 6;
 	const kWbClassThaiLetter =       7;
-
 	
-	var _pdfConverterVersion = null;
-	var _pdfConverterFileName = null;
-	var _pdfConverterScript = null; // nsIFile of hidden window script on Windows
 	var _pdfConverter = null; // nsIFile to executable
-	var _pdfInfoVersion = null;
-	var _pdfInfoFileName = null;
-	var _pdfInfoScript = null; // nsIFile of redirection script
 	var _pdfInfo = null; // nsIFile to executable
+	var _pdfData = null;
 	
 	var _idleObserverIsRegistered = false;
 	var _idleObserverDelay = 30;
@@ -84,22 +69,34 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 		
 		this.decoder = Components.classes["@mozilla.org/intl/utf8converterservice;1"].
 			getService(Components.interfaces.nsIUTF8ConverterService);
-
-		var platform = Zotero.platform.replace(/ /g, '-');
-		_pdfConverterFileName = this.pdfConverterName + '-' + platform;
-		_pdfInfoFileName = this.pdfInfoName + '-' + platform;
+		
+		let pdfConverterFileName = "pdftotext";
+		let pdfInfoFileName = "pdfinfo";
+		
 		if (Zotero.isWin) {
-			_pdfConverterFileName += '.exe';
-			_pdfInfoFileName += '.exe';
+			pdfConverterFileName += '.exe';
+			pdfInfoFileName += '.exe';
 		}
 		
-		this.__defineGetter__("pdfConverterFileName", function() { return _pdfConverterFileName; });
-		this.__defineGetter__("pdfConverterVersion", function() { return _pdfConverterVersion; });
-		this.__defineGetter__("pdfInfoFileName", function() { return _pdfInfoFileName; });
-		this.__defineGetter__("pdfInfoVersion", function() { return _pdfInfoVersion; });
+		let dir = FileUtils.getDir('AChrom', []).parent;
 		
-		yield this.registerPDFTool('converter');
-		yield this.registerPDFTool('info');
+		_pdfData = dir.clone();
+		_pdfData.append('poppler-data');
+		_pdfData = _pdfData.path;
+		
+		_pdfConverter = dir.clone();
+		_pdfInfo = dir.clone();
+		
+		if(Zotero.isMac) {
+			_pdfConverter = _pdfConverter.parent;
+			_pdfConverter.append('MacOS');
+			
+			_pdfInfo = _pdfInfo.parent;
+			_pdfInfo.append('MacOS');
+		}
+
+		_pdfConverter.append(pdfConverterFileName);
+		_pdfInfo.append(pdfInfoFileName);
 		
 		Zotero.uiReadyPromise.delay(30000).then(() => {
 			this.registerContentProcessor();
@@ -134,6 +131,22 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 	});
 	
 	
+	this.setPDFConverterPath = function(path) {
+		_pdfConverter = Zotero.File.pathToFile(path);
+	};
+	
+	
+	this.setPDFInfoPath = function(path) {
+		_pdfInfo = Zotero.File.pathToFile(path);
+		
+	};
+	
+	
+	this.setPDFDataPath = function(path) {
+		_pdfData = path;
+	};
+	
+	
 	this.getLibraryVersion = function (libraryID) {
 		if (!libraryID) throw new Error("libraryID not provided");
 		return Zotero.DB.valueQueryAsync(
@@ -197,279 +210,12 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 	}
 	
 	
-	this.getLatestPDFToolsVersion = Zotero.Promise.coroutine(function* () {
-		if (Zotero.isWin) {
-			return "3.02a";
-		}
-		
-		// Find latest version for this platform
-		var url = Zotero.Fulltext.pdfToolsDownloadBaseURL + 'latest.json';
-		var xmlhttp = yield Zotero.HTTP.request("GET", url, { responseType: "json" });
-		var json = xmlhttp.response;
-		
-		var platform = Zotero.platform.replace(/\s/g, '-');
-		var version = json[platform] || json['default'];
-		
-		Zotero.debug("Latest PDF tools version for " + platform + " is " + version);
-		
-		return version;
-	});
-	
-	
-	/*
-	 * Download and install latest PDF tool
-	 */
-	this.downloadPDFTool = Zotero.Promise.coroutine(function* (tool, version) {
-		var ioService = Components.classes["@mozilla.org/network/io-service;1"]
-			.getService(Components.interfaces.nsIIOService);
-		
-		if (tool == 'converter') {
-			var fileName = this.pdfConverterFileName;
-		}
-		else {
-			var fileName = this.pdfInfoFileName;
-		}
-		
-		var spec = this.pdfToolsDownloadBaseURL + version + "/" + fileName;
-		var uri = ioService.newURI(spec, null, null);
-		var tmpFile = OS.Path.join(Zotero.getTempDirectory().path, fileName);
-		
-		yield Zotero.File.download(uri, tmpFile);
-		
-		var fileInfo = yield OS.File.stat(tmpFile);
-		
-		// Delete if too small, since a 404 might not be detected above
-		if (fileInfo.size < 50000) {
-			let msg = tmpFile + " is too small -- deleting";
-			Zotero.logError(msg);
-			try {
-				yield OS.File.remove(tmpFile);
-			}
-			catch (e) {
-				Zotero.logError(e);
-			}
-			throw new Error(msg);
-		}
-		
-		var scriptExt = _getScriptExtension();
-		// On Windows, write out script to hide pdftotext console window
-		// TEMP: disabled
-		if (false && tool == 'converter') {
-			if (Zotero.isWin) {
-				let content = yield Zotero.File.getContentsFromURLAsync(
-					'resource://zotero/hide.' + scriptExt
-				);
-				var tmpScriptFile = OS.Path.join(
-					Zotero.getTempDirectory().path,
-					'pdftotext.' + scriptExt
-				);
-				yield Zotero.File.putContentsAsync(tmpScriptFile, content);
-			}
-		}
-		// Write out output redirection script for pdfinfo
-		// TEMP: disabled on Windows
-		else if (!Zotero.isWin && tool == 'info') {
-			let content = yield Zotero.File.getContentsFromURLAsync(
-				'resource://zotero/redirect.' + scriptExt
-			);
-			var tmpScriptFile = OS.Path.join(
-				Zotero.getTempDirectory().path,
-				'pdfinfo.' + scriptExt
-			);
-			yield Zotero.File.putContentsAsync(tmpScriptFile, content);
-		}
-		
-		// Set permissions to 755
-		if (Zotero.isMac || Zotero.isLinux) {
-			yield OS.File.setPermissions(tmpFile, {
-				unixMode: 0o755
-			});
-			if (tmpScriptFile) {
-				yield OS.File.setPermissions(tmpScriptFile, {
-					unixMode: 0o755
-				});
-			}
-		}
-		
-		var destDir = Zotero.File.pathToFile(Zotero.DataDirectory.dir);
-		// Move redirect script and executable into data dir
-		if (tmpScriptFile) {
-			yield OS.File.move(
-				tmpScriptFile,
-				OS.Path.join(destDir.path, OS.Path.basename(tmpScriptFile))
-			);
-		}
-		yield OS.File.move(tmpFile, OS.Path.join(destDir.path, fileName));
-		
-		// Write the version number to a file
-		var versionFile = destDir.clone();
-		versionFile.append(fileName + '.version');
-		// TEMP
-		if (Zotero.isWin) {
-			version = '3.02a';
-		}
-		yield Zotero.File.putContentsAsync(versionFile, version + '');
-		
-		yield Zotero.Fulltext.registerPDFTool(tool);
-	});
-	
-	
-	/*
-	 * Looks for pdftotext-{platform}[.exe] in the Zotero data directory
-	 *
-	 * {platform} is navigator.platform, with spaces replaced by hyphens
-	 *   e.g. "Win32", "Linux-i686", "MacPPC", "MacIntel", etc.
-	 */
-	this.registerPDFTool = Zotero.Promise.coroutine(function* (tool) {
-		var errMsg = false;
-		var exec = Zotero.File.pathToFile(Zotero.DataDirectory.dir);
-		
-		switch (tool) {
-			case 'converter':
-				var toolName = this.pdfConverterName;
-				var fileName = _pdfConverterFileName;
-				break;
-				
-			case 'info':
-				var toolName = this.pdfInfoName;
-				var fileName = _pdfInfoFileName;
-				break;
-			
-			default:
-				throw ("Invalid PDF tool type '" + tool + "' in Zotero.Fulltext.registerPDFTool()");
-		}
-		
-		exec.append(fileName);
-		if (!exec.exists()) {
-			exec = null;
-			errMsg = fileName + ' not found';
-		}
-		
-		if (!exec) {
-			if (tool == 'converter') {
-				Zotero.debug(errMsg + ' -- PDF indexing disabled');
-			}
-			return false;
-		}
-		
-		var versionFile = exec.parent;
-		versionFile.append(fileName + '.version');
-		if (versionFile.exists()) {
-			try {
-				var version = (yield Zotero.File.getSample(versionFile)).split(/[\r\n\s]/)[0];
-			}
-			catch (e) {
-				Zotero.debug(e, 1);
-				Components.utils.reportError(e);
-			}
-		}
-		if (!version) {
-			var version = 'UNKNOWN';
-		}
-		
-		// If scripts exist, use those instead
-		switch (tool) {
-		case 'converter':
-			// TEMP: disabled
-			if (false && Zotero.isWin) {
-				var script = Zotero.File.pathToFile(Zotero.DataDirectory.dir);
-				script.append('pdftotext.' + _getScriptExtension())
-				if (script.exists()) {
-					Zotero.debug(script.leafName + " registered");
-					_pdfConverterScript = script;
-				}
-			}
-			break;
-		
-		case 'info':
-			// Modified 3.02 version doesn't use redirection script
-			if (version.startsWith('3.02')) break;
-			
-			var script = Zotero.File.pathToFile(Zotero.DataDirectory.dir);
-			// TEMP: disabled on Win
-			if (!Zotero.isWin) {
-				script.append('pdfinfo.' + _getScriptExtension())
-				// The redirection script is necessary to run pdfinfo
-				if (!script.exists()) {
-					Zotero.debug(script.leafName + " not found -- PDF statistics disabled");
-					return false;
-				}
-				Zotero.debug(toolName + " redirection script registered");
-				_pdfInfoScript = script;
-			}
-			break;
-		}
-		
-		switch (tool) {
-			case 'converter':
-				_pdfConverter = exec;
-				_pdfConverterVersion = version;
-				break;
-				
-			case 'info':
-				_pdfInfo = exec;
-				_pdfInfoVersion = version;
-				break;
-		}
-		
-		Zotero.debug(toolName + ' version ' + version + ' registered');
-		
-		return true;
-	});
-	
-	
-	/**
-	 * Unregister and delete PDF tools
-	 *
-	 * Used only for tests
-	 */
-	this.uninstallPDFTools = Zotero.Promise.coroutine(function* () {
-		Zotero.debug("Uninstalling PDF tools");
-		
-		if (_pdfConverter) {
-			yield Zotero.File.removeIfExists(_pdfConverter.path);
-			yield Zotero.File.removeIfExists(_pdfConverter.path + ".version");
-		}
-		if (_pdfInfo) {
-			yield Zotero.File.removeIfExists(_pdfInfo.path);
-			yield Zotero.File.removeIfExists(_pdfInfo.path + ".version");
-		}
-		if (_pdfConverterScript) yield Zotero.File.removeIfExists(_pdfConverterScript.path);
-		if (_pdfInfoScript) yield Zotero.File.removeIfExists(_pdfInfoScript.path);
-		
-		_pdfConverter = null;
-		_pdfInfo = null;
-		_pdfInfoScript = null;
-	});
-	
-	
-	function pdfConverterIsRegistered() {
-		return !!_pdfConverter;
-	}
-	
-	
-	function pdfInfoIsRegistered() {
-		return !!_pdfInfo;
-	}
-	
-	
 	this.getPDFConverterExecAndArgs = function () {
-		if (!this.pdfConverterIsRegistered()) {
-			throw new Error("PDF converter is not registered");
-		}
-		
-		if (_pdfConverterScript) {
-			return {
-				exec: _pdfConverterScript,
-				args: [_pdfConverter.path]
-			}
-		}
-		
 		return {
 			exec: _pdfConverter,
-			args: []
+			args: ['-datadir', _pdfData]
 		}
-	}
+	};
 	
 	
 	/*
@@ -515,6 +261,10 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 	var indexString = Zotero.Promise.coroutine(function* (text, charset, itemID, stats, version, synced) {
 		var words = this.semanticSplitter(text, charset);
 		
+		while (Zotero.DB.inTransaction()) {
+			yield Zotero.DB.waitForTransaction('indexString()');
+		}
+		
 		yield Zotero.DB.executeTransaction(function* () {
 			this.clearItemWords(itemID, true);
 			yield indexWords(itemID, words, stats, version, synced);
@@ -674,11 +424,6 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 	 * @return {Promise}
 	 */
 	this.indexPDF = Zotero.Promise.coroutine(function* (filePath, itemID, allPages) {
-		if (!_pdfConverter) {
-			Zotero.debug("PDF tools are not installed -- skipping indexing");
-			return false;
-		}
-		
 		var maxPages = Zotero.Prefs.get('fulltext.pdfMaxPages');
 		if (maxPages == 0) {
 			return false;
@@ -697,38 +442,21 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 		var infoFilePath = OS.Path.join(parentDirPath, this.pdfInfoCacheFile);
 		var cacheFilePath = OS.Path.join(parentDirPath, this.pdfConverterCacheFile);
 		
-		// Modified 3.02 version that can output a text file directly
-		if (_pdfInfo && _pdfInfoVersion.startsWith('3.02')) {
-			let args = [filePath, infoFilePath];
-			
-			try {
-				yield Zotero.Utilities.Internal.exec(_pdfInfo, args);
-				var totalPages = yield getTotalPagesFromFile(itemID);
-			}
-			catch (e) {
-				Zotero.debug("Error running pdfinfo");
-			}
+
+		var args = [filePath, infoFilePath];
+
+		try {
+			yield Zotero.Utilities.Internal.exec(_pdfInfo, args);
+			var totalPages = yield getTotalPagesFromFile(itemID);
 		}
-		// Use redirection script
-		else if (_pdfInfoScript) {
-			let args = [_pdfInfo.path, filePath, infoFilePath];
-			
-			try {
-				yield Zotero.Utilities.Internal.exec(_pdfInfoScript, args);
-				var totalPages = yield getTotalPagesFromFile(itemID);
-			}
-			catch (e) {
-				Components.utils.reportError(e);
-				Zotero.debug("Error running pdfinfo", 1);
-				Zotero.debug(e, 1);
-			}
-		}
-		else {
-			Zotero.debug(this.pdfInfoName + " is not available");
+		catch (e) {
+			Zotero.debug("Error running " + _pdfInfo.path, 1);
+			Zotero.logError(e);
 		}
+
 		
 		var {exec, args} = this.getPDFConverterExecAndArgs();
-		args.push('-enc', 'UTF-8', '-nopgbrk');
+		args.push('-nopgbrk');
 		
 		if (allPages) {
 			if (totalPages) {
@@ -745,9 +473,8 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 			yield Zotero.Utilities.Internal.exec(exec, args);
 		}
 		catch (e) {
-			Components.utils.reportError(e);
-			Zotero.debug("Error running pdftotext", 1);
-			Zotero.debug(e, 1);
+			Zotero.debug("Error running " + exec.path, 1);
+			Zotero.logError(e);
 			return false;
 		}
 		
@@ -800,22 +527,61 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 				continue;
 			}
 			
-			if (ignoreErrors) {
-				try {
-					yield indexFile(path, item.attachmentContentType, item.attachmentCharset, itemID, complete);
-				}
-				catch (e) {
+			try {
+				yield indexFile(path, item.attachmentContentType, item.attachmentCharset, itemID, complete);
+			}
+			catch (e) {
+				if (ignoreErrors) {
 					Components.utils.reportError("Error indexing " + path);
 					Zotero.logError(e);
 				}
-			}
-			else {
-				yield indexFile(path, item.attachmentContentType, item.attachmentCharset, itemID, complete);
+				else {
+					throw e;
+				}
 			}
 		}
 	});
 	
 	
+	// TEMP: Temporary mechanism to serialize indexing of new attachments
+	//
+	// This should instead save the itemID to a table that's read by the content processor
+	var _queue = [];
+	var _indexing = false;
+	var _nextIndexTime;
+	var _indexDelay = 5000;
+	var _indexInterval = 500;
+	this.queueItem = function (item) {
+		// Don't index files in the background during tests
+		if (Zotero.test) return;
+		
+		_queue.push(item.id);
+		_nextIndexTime = Date.now() + _indexDelay;
+		setTimeout(() => {
+			_processNextItem()
+		}, _indexDelay);
+	};
+	
+	async function _processNextItem() {
+		if (!_queue.length) return;
+		// Another _processNextItem() was scheduled
+		if (Date.now() < _nextIndexTime) return;
+		// If indexing is already running, _processNextItem() will be called when it's done
+		if (_indexing) return;
+		_indexing = true;
+		var itemID = _queue.shift();
+		try {
+			await Zotero.Fulltext.indexItems([itemID], false, true);
+		}
+		finally {
+			_indexing = false;
+		}
+		setTimeout(() => {
+			_processNextItem();
+		}, _indexInterval);
+	};
+	
+	
 	//
 	// Full-text content syncing
 	//
@@ -849,7 +615,7 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 			let item = yield Zotero.Items.getAsync(itemID);
 			let libraryKey = item.libraryKey;
 			let contentType = item.attachmentContentType;
-			if (isCachedMIMEType(contentType) || Zotero.MIME.isTextType(contentType)) {
+			if (contentType && (isCachedMIMEType(contentType) || Zotero.MIME.isTextType(contentType))) {
 				try {
 					let cacheFile = this.getItemCacheFile(item).path;
 					if (yield OS.File.exists(cacheFile)) {
@@ -904,7 +670,7 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 			}
 			else {
 				Zotero.debug("Skipping non-text file getting full-text content for item "
-					+ libraryKey, 2);
+					+ `${libraryKey} (contentType: ${contentType})`, 2);
 				
 				// Delete rows for items that weren't supposed to be indexed
 				yield Zotero.DB.executeTransaction(function* () {
@@ -1054,6 +820,8 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 	 * Start the idle observer for the background content processor
 	 */
 	this.registerContentProcessor = function () {
+		// Don't start idle observer during tests
+		if (Zotero.test) return;
 		if (!Zotero.Prefs.get('sync.fulltext.enabled')) return;
 		
 		if (!_idleObserverIsRegistered) {
@@ -1624,7 +1392,12 @@ Zotero.Fulltext = Zotero.FullText = new function(){
 	 * Item must be a non-web-link attachment that isn't already fully indexed
 	 */
 	this.canReindex = Zotero.Promise.coroutine(function* (item) {
-		if (item.isAttachment() && item.attachmentLinkMode != Zotero.Attachments.LINK_MODE_LINKED_URL) {
+		if (item.isAttachment()
+				&& item.attachmentLinkMode != Zotero.Attachments.LINK_MODE_LINKED_URL) {
+			let contentType = item.attachmentContentType;
+			if (!contentType || contentType != 'application/pdf' && !Zotero.MIME.isTextType(contentType)) {
+				return false;
+			}
 			switch (yield this.getIndexedState(item)) {
 				case this.INDEX_STATE_UNAVAILABLE:
 				case this.INDEX_STATE_UNINDEXED:

chrome/content/zotero/xpcom/http.js

@@ -12,6 +12,8 @@ Zotero.HTTP = new function() {
 	this.UnexpectedStatusException = function(xmlhttp, msg) {
 		this.xmlhttp = xmlhttp;
 		this.status = xmlhttp.status;
+		this.channelStatus = null;
+		this.responseStatus = null;
 		this.channel = xmlhttp.channel;
 		this.message = msg;
 		this.stack = new Error().stack;
@@ -33,6 +35,24 @@ Zotero.HTTP = new function() {
 		catch (e) {
 			Zotero.debug(e, 1);
 		}
+		
+		// If the connection failed, try to find out what really happened
+		if (!this.status) {
+			try {
+				if (xmlhttp.channel.status) {
+					this.channelStatus = xmlhttp.channel.status;
+					Zotero.debug("Channel status was " + this.channelStatus, 2);
+				}
+			}
+			catch (e) {}
+			try {
+				if (xmlhttp.channel.responseStatus) {
+					this.responseStatus = xmlhttp.channel.responseStatus;
+					Zotero.debug("Response status was " + this.responseStatus, 2);
+				}
+			}
+			catch (e) {}
+		}
 	};
 	this.UnexpectedStatusException.prototype = Object.create(Error.prototype);
 	this.UnexpectedStatusException.prototype.is4xx = function () {
@@ -174,8 +194,13 @@ Zotero.HTTP = new function() {
 			channel.forceAllowThirdPartyCookie = true;
 			
 			// Set charset
+			//
+			// This is the method used in the connector, but as noted there, this parameter is a
+			// legacy of XPCOM functionality (where it could be set on the nsIChannel, which
+			// doesn't seem to work anymore), and we should probably allow responseContentType to
+			// be set instead
 			if (options.responseCharset) {
-				channel.contentCharset = responseCharset;
+				xmlhttp.overrideMimeType(`text/plain; charset=${responseCharset}`);
 			}
 			
 			// Disable caching if requested
@@ -243,6 +268,18 @@ Zotero.HTTP = new function() {
 		xmlhttp.onloadend = function() {
 			var status = xmlhttp.status;
 			
+			// If an invalid HTTP response (e.g., NS_ERROR_INVALID_CONTENT_ENCODING) includes a
+			// 4xx or 5xx HTTP response code, swap it in, since it might be enough info to do
+			// what we need (e.g., verify a 404 from a WebDAV server)
+			try {
+				if (!status && xmlhttp.channel.responseStatus >= 400) {
+					Zotero.warn(`Overriding status for invalid response for ${dispURL} `
+						+ `(${xmlhttp.channel.status})`);
+					status = xmlhttp.channel.responseStatus;
+				}
+			}
+			catch (e) {}
+			
 			if (options.successCodes) {
 				var success = options.successCodes.indexOf(status) != -1;
 			}
@@ -259,13 +296,13 @@ Zotero.HTTP = new function() {
 			
 			if(success) {
 				Zotero.debug("HTTP " + method + " " + dispURL
-					+ " succeeded with " + xmlhttp.status);
+					+ " succeeded with " + status);
 				if (options.debug) {
 					Zotero.debug(xmlhttp.responseText);
 				}
 				deferred.resolve(xmlhttp);
 			} else {
-				let msg = "HTTP " + method + " " + dispURL + " failed with status code " + xmlhttp.status;
+				let msg = "HTTP " + method + " " + dispURL + " failed with status code " + status;
 				if (!xmlhttp.responseType && xmlhttp.responseText) {
 					msg += ":\n\n" + xmlhttp.responseText;
 				}
@@ -342,9 +379,9 @@ Zotero.HTTP = new function() {
 		channel.QueryInterface(Components.interfaces.nsIHttpChannelInternal);
 		channel.forceAllowThirdPartyCookie = true;
 		
-		// Set charset
+		// Set charset -- see note in request() above
 		if (responseCharset) {
-			channel.contentCharset = responseCharset;
+			xmlhttp.overrideMimeType(`text/plain; charset=${responseCharset}`);
 		}
 		
 		// Set request headers
@@ -360,7 +397,7 @@ Zotero.HTTP = new function() {
 		var useMethodjit = Components.utils.methodjit;
 		/** @ignore */
 		xmlhttp.onreadystatechange = function() {
-			_stateChange(xmlhttp, onDone, responseCharset);
+			_stateChange(xmlhttp, onDone);
 		};
 		
 		if(cookieSandbox) cookieSandbox.attachToInterfaceRequestor(xmlhttp.getInterface(Components.interfaces.nsIInterfaceRequestor));
@@ -414,9 +451,9 @@ Zotero.HTTP = new function() {
 		channel.QueryInterface(Components.interfaces.nsIHttpChannelInternal);
 		channel.forceAllowThirdPartyCookie = true;
 		
-		// Set charset
+		// Set charset -- see note in request() above
 		if (responseCharset) {
-			channel.contentCharset = responseCharset;
+			xmlhttp.overrideMimeType(`text/plain; charset=${responseCharset}`);
 		}
 		
 		if (headers) {
@@ -444,7 +481,7 @@ Zotero.HTTP = new function() {
 		var useMethodjit = Components.utils.methodjit;
 		/** @ignore */
 		xmlhttp.onreadystatechange = function() {
-			_stateChange(xmlhttp, onDone, responseCharset);
+			_stateChange(xmlhttp, onDone);
 		};
 		
 		if(cookieSandbox) cookieSandbox.attachToInterfaceRequestor(xmlhttp.getInterface(Components.interfaces.nsIInterfaceRequestor));
@@ -988,11 +1025,10 @@ Zotero.HTTP = new function() {
 	 *
 	 * @param {nsIXMLHttpRequest} xmlhttp XMLHttpRequest whose state just changed
 	 * @param {Function} [callback] Callback for request completion
-	 * @param {String} [responseCharset] Character set to force on the response
 	 * @param {*} [data] Data to be passed back to callback as the second argument
 	 * @private
 	 */
-	function _stateChange(xmlhttp, callback, responseCharset, data) {
+	function _stateChange(xmlhttp, callback, data) {
 		switch (xmlhttp.readyState){
 			// Request not yet made
 			case 1:
@@ -1008,10 +1044,6 @@ Zotero.HTTP = new function() {
 			// Download complete
 			case 4:
 				if (callback) {
-					// Override the content charset
-					if (responseCharset) {
-						xmlhttp.channel.contentCharset = responseCharset;
-					}
 					callback(xmlhttp, data);
 				}
 			break;
@@ -1024,6 +1056,9 @@ Zotero.HTTP = new function() {
 		}
 		
 		let secInfo = channel.securityInfo;
+		let msg;
+		let dialogButtonText;
+		let dialogButtonCallback;
 		if (secInfo instanceof Ci.nsITransportSecurityInfo) {
 			secInfo.QueryInterface(Ci.nsITransportSecurityInfo);
 			if ((secInfo.securityState & Ci.nsIWebProgressListener.STATE_IS_INSECURE)
@@ -1052,13 +1087,15 @@ Zotero.HTTP = new function() {
 					== Ci.nsIWebProgressListener.STATE_IS_BROKEN) {
 				msg = Zotero.getString('sync.error.sslConnectionError');
 			}
-			throw new Zotero.HTTP.SecurityException(
-				msg,
-				{
-					dialogButtonText,
-					dialogButtonCallback
-				}
-			);
+			if (msg) {
+				throw new Zotero.HTTP.SecurityException(
+					msg,
+					{
+						dialogButtonText,
+						dialogButtonCallback
+					}
+				);
+			}
 		}
 	}
 

chrome/content/zotero/xpcom/itemTreeView.js

@@ -67,22 +67,18 @@ Zotero.ItemTreeView.prototype.regularOnly = false;
 Zotero.ItemTreeView.prototype.expandAll = false;
 Zotero.ItemTreeView.prototype.collapseAll = false;
 
+Object.defineProperty(Zotero.ItemTreeView.prototype, 'window', {
+	get: function () {
+		return this._ownerDocument.defaultView;
+	},
+	enumerable: true
+});
 
 /**
  * Called by the tree itself
  */
 Zotero.ItemTreeView.prototype.setTree = async function (treebox) {
 	try {
-		Zotero.debug("Setting tree for " + this.collectionTreeRow.id + " items view " + this.id);
-		var start = Date.now();
-		// Try to set the window document if not yet set
-		if (treebox && !this._ownerDocument) {
-			try {
-				this._ownerDocument = treebox.treeBody.ownerDocument;
-			}
-			catch (e) {}
-		}
-		
 		if (this._treebox) {
 			if (this._needsSort) {
 				this.sort();
@@ -90,28 +86,39 @@ Zotero.ItemTreeView.prototype.setTree = async function (treebox) {
 			return;
 		}
 		
+		var start = Date.now();
+		
+		Zotero.debug("Setting tree for " + this.collectionTreeRow.id + " items view " + this.id);
+		
 		if (!treebox) {
 			Zotero.debug("Treebox not passed in setTree()", 2);
 			return;
 		}
+		this._treebox = treebox;
 		
 		if (!this._ownerDocument) {
-			Zotero.debug("No owner document in setTree()", 2);
-			return;
+			try {
+				this._ownerDocument = treebox.treeBody.ownerDocument;
+			}
+			catch (e) {}
+			
+			if (!this._ownerDocument) {
+				Zotero.debug("No owner document in setTree()", 2);
+				return;
+			}
 		}
 		
-		this._treebox = treebox;
 		this.setSortColumn();
 		
-		if (this._ownerDocument.defaultView.ZoteroPane_Local) {
-			this._ownerDocument.defaultView.ZoteroPane_Local.setItemsPaneMessage(Zotero.getString('pane.items.loading'));
+		if (this.window.ZoteroPane) {
+			this.window.ZoteroPane.setItemsPaneMessage(Zotero.getString('pane.items.loading'));
 		}
 		
 		if (Zotero.locked) {
 			Zotero.debug("Zotero is locked -- not loading items tree", 2);
 			
-			if (this._ownerDocument.defaultView.ZoteroPane_Local) {
-				this._ownerDocument.defaultView.ZoteroPane_Local.clearItemsPaneMessage();
+			if (this.window.ZoteroPane) {
+				this.window.ZoteroPane.clearItemsPaneMessage();
 			}
 			return;
 		}
@@ -185,6 +192,7 @@ Zotero.ItemTreeView.prototype.setTree = async function (treebox) {
 			}
 			
 			event.preventDefault();
+			event.stopPropagation();
 			
 			Zotero.spawn(function* () {
 				if (coloredTagsRE.test(key)) {
@@ -464,7 +472,7 @@ Zotero.ItemTreeView.prototype.refresh = Zotero.serial(Zotero.Promise.coroutine(f
 		
 		// Clear My Publications intro text on a refresh with items
 		if (this.collectionTreeRow.isPublications() && this.rowCount) {
-			this._ownerDocument.defaultView.ZoteroPane_Local.clearItemsPaneMessage();
+			this.window.ZoteroPane.clearItemsPaneMessage();
 		}
 		
 		yield this.runListeners('refresh');
@@ -621,7 +629,8 @@ Zotero.ItemTreeView.prototype.notify = Zotero.Promise.coroutine(function* (actio
 	var zp = Zotero.getActiveZoteroPane();
 	var activeWindow = zp && zp.itemsView == this;
 	
-	var quicksearch = this._ownerDocument.getElementById('zotero-tb-search');
+	var quickSearch = this._ownerDocument.getElementById('zotero-tb-search');
+	var hasQuickSearch = quickSearch && quickSearch.value != '';
 	
 	// 'collection-item' ids are in the form collectionID-itemID
 	if (type == 'collection-item') {
@@ -648,7 +657,7 @@ Zotero.ItemTreeView.prototype.notify = Zotero.Promise.coroutine(function* (actio
 	}
 	
 	this.selection.selectEventsSuppressed = true;
-	//this._treebox.beginUpdateBatch();
+	this._treebox.beginUpdateBatch();
 	
 	if ((action == 'remove' && !collectionTreeRow.isLibrary(true))
 			|| action == 'delete' || action == 'trash'
@@ -698,7 +707,8 @@ Zotero.ItemTreeView.prototype.notify = Zotero.Promise.coroutine(function* (actio
 		// If saved search, publications, or trash, just re-run search
 		if (collectionTreeRow.isSearch()
 				|| collectionTreeRow.isPublications()
-				|| collectionTreeRow.isTrash()) {
+				|| collectionTreeRow.isTrash()
+				|| hasQuickSearch) {
 			let skipExpandMatchParents = collectionTreeRow.isPublications();
 			yield this.refresh(skipExpandMatchParents);
 			refreshed = true;
@@ -709,14 +719,11 @@ Zotero.ItemTreeView.prototype.notify = Zotero.Promise.coroutine(function* (actio
 				sort = true;
 			}
 		}
-		
 		else if (collectionTreeRow.isFeed()) {
-			this._ownerDocument.defaultView.ZoteroItemPane.setToggleReadLabel();
+			this.window.ZoteroPane.updateReadLabel();
 		}
-		
-		// If no quicksearch, process modifications manually
-		else if (!quicksearch || quicksearch.value == '')
-		{
+		// If not a search, process modifications manually
+		else {
 			var items = Zotero.Items.get(ids);
 			
 			for (let i = 0; i < items.length; i++) {
@@ -796,33 +803,6 @@ Zotero.ItemTreeView.prototype.notify = Zotero.Promise.coroutine(function* (actio
 				sort = true;
 			}
 		}
-		
-		// If quicksearch, re-run it, since the results may have changed
-		else
-		{
-			var allDeleted = true;
-			var isTrash = collectionTreeRow.isTrash();
-			var items = Zotero.Items.get(ids);
-			for (let item of items) {
-				// If not viewing trash and all items were deleted, ignore modify
-				if (allDeleted && !isTrash && !item.deleted) {
-					allDeleted = false;
-				}
-			}
-			
-			if (!allDeleted) {
-				quicksearch.doCommand();
-				// See _refreshPromise note below
-				if (this._refreshPromise) {
-					try {
-						yield this._refreshPromise;
-					}
-					catch (e) {}
-				}
-				madeChanges = true;
-				sort = true;
-			}
-		}
 	}
 	else if(type == 'item' && action == 'add')
 	{
@@ -832,16 +812,32 @@ Zotero.ItemTreeView.prototype.notify = Zotero.Promise.coroutine(function* (actio
 		if (collectionTreeRow.isSearch()
 				|| collectionTreeRow.isPublications()
 				|| collectionTreeRow.isTrash()
-				|| collectionTreeRow.isUnfiled()) {
+				|| collectionTreeRow.isUnfiled()
+				|| hasQuickSearch) {
+			if (hasQuickSearch) {
+				// For item adds, clear the quick search, unless all the new items have
+				// skipSelect or are child items
+				if (activeWindow && type == 'item') {
+					let clear = false;
+					for (let i=0; i<items.length; i++) {
+						if (!extraData[items[i].id].skipSelect && items[i].isTopLevelItem()) {
+							clear = true;
+							break;
+						}
+					}
+					if (clear) {
+						quickSearch.value = '';
+						collectionTreeRow.setSearch('');
+					}
+				}
+			}
 			yield this.refresh();
 			refreshed = true;
 			madeChanges = true;
 			sort = true;
 		}
-		
-		// If not a quicksearch, process new items manually
-		else if (!quicksearch || quicksearch.value == '')
-		{
+		// Otherwise process new items manually
+		else {
 			for (let i=0; i<items.length; i++) {
 				let item = items[i];
 				// if the item belongs in this collection
@@ -861,36 +857,6 @@ Zotero.ItemTreeView.prototype.notify = Zotero.Promise.coroutine(function* (actio
 				sort = (items.length == 1) ? items[0].id : true;
 			}
 		}
-		// Otherwise re-run the quick search, which refreshes the item list
-		else
-		{
-			// For item adds, clear the quicksearch, unless all the new items have skipSelect or are
-			// child items
-			if (activeWindow && type == 'item') {
-				let clear = false;
-				for (let i=0; i<items.length; i++) {
-					if (!extraData[items[i].id].skipSelect && items[i].isTopLevelItem()) {
-						clear = true;
-						break;
-					}
-				}
-				if (clear) {
-					quicksearch.value = '';
-				}
-			}
-			quicksearch.doCommand();
-			// We have to wait for the search in order to select new items properly, but doCommand()
-			// doesn't provide the return value from the oncommand handler, so we can't wait for an
-			// asynchronous handler. But really they just end up calling refresh(), so we wait for that.
-			if (this._refreshPromise) {
-				try {
-					yield this._refreshPromise;
-				}
-				catch (e) {}
-			}
-			madeChanges = true;
-			sort = true;
-		}
 	}
 	
 	var reselect = false;
@@ -1019,7 +985,7 @@ Zotero.ItemTreeView.prototype.notify = Zotero.Promise.coroutine(function* (actio
 	
 	this._updateIntroText();
 	
-	//this._treebox.endUpdateBatch();
+	this._treebox.endUpdateBatch();
 	
 	// If we made changes to the selection (including reselecting the same item, which will register as
 	// a selection when selectEventsSuppressed is set to false), wait for a select event on the tree
@@ -1323,7 +1289,7 @@ Zotero.ItemTreeView.prototype.toggleOpenState = function (row, skipRowMapRefresh
 	this._treebox.invalidateRow(row);
 	
 	if (!skipRowMapRefresh) {
-		Zotero.debug('Refreshing hash map');
+		Zotero.debug('Refreshing item row map');
 		this._refreshItemRowMap();
 	}
 }
@@ -1356,7 +1322,7 @@ Zotero.ItemTreeView.prototype._closeContainer = function (row, skipRowMapRefresh
 	this._treebox.invalidateRow(row);
 	
 	if (!skipRowMapRefresh) {
-		Zotero.debug('Refreshing hash map');
+		Zotero.debug('Refreshing item row map');
 		this._refreshItemRowMap();
 	}
 }
@@ -1460,9 +1426,10 @@ Zotero.ItemTreeView.prototype.sort = function (itemIDs) {
 		
 		for (let i = parentRows.length - 1; i >= 0; i--) {
 			let row = parentRows[i];
-			this._closeContainer(row);
-			this.toggleOpenState(row);
+			this._closeContainer(row, true);
+			this.toggleOpenState(row, true);
 		}
+		this._refreshItemRowMap();
 		
 		let numSorted = itemIDs.length - skipped.length;
 		if (numSorted) {
@@ -1722,7 +1689,7 @@ Zotero.ItemTreeView.prototype.sort = function (itemIDs) {
  * Show intro text in middle pane for some views when no items
  */
 Zotero.ItemTreeView.prototype._updateIntroText = function() {
-	if (!this._ownerDocument.defaultView.ZoteroPane) {
+	if (!this.window.ZoteroPane) {
 		return;
 	}
 	
@@ -1821,7 +1788,7 @@ Zotero.ItemTreeView.prototype._updateIntroText = function() {
 	}
 	
 	if (this._introText || this._introText === null) {
-		this._ownerDocument.defaultView.ZoteroPane_Local.clearItemsPaneMessage();
+		this.window.ZoteroPane.clearItemsPaneMessage();
 		this._introText = false;
 	}
 };
@@ -1880,10 +1847,10 @@ Zotero.ItemTreeView.prototype.selectItem = Zotero.Promise.coroutine(function* (i
 		if (!parent || parentRow === null) {
 			// No parent -- it's not here
 			
-			// Clear the quicksearch and tag selection and try again (once)
-			if (!noRecurse && this._ownerDocument.defaultView.ZoteroPane_Local) {
-				let cleared1 = yield this._ownerDocument.defaultView.ZoteroPane_Local.clearQuicksearch();
-				let cleared2 = this._ownerDocument.defaultView.ZoteroPane_Local.clearTagSelection();
+			// Clear the quick search and tag selection and try again (once)
+			if (!noRecurse && this.window.ZoteroPane) {
+				let cleared1 = yield this.window.ZoteroPane.clearQuicksearch();
+				let cleared2 = this.window.ZoteroPane.clearTagSelection();
 				if (cleared1 || cleared2) {
 					return this.selectItem(id, expand, true);
 				}
@@ -1909,20 +1876,29 @@ Zotero.ItemTreeView.prototype.selectItem = Zotero.Promise.coroutine(function* (i
 	// refreshed. To get around this, we wait for a select event that's triggered by
 	// itemSelected() when it's done.
 	let promise;
-	if (this.selection.selectEventsSuppressed) {
+	try {
+		if (this.selection.selectEventsSuppressed) {
+			this.selection.select(row);
+		}
+		else {
+			promise = this.waitForSelect();
+			this.selection.select(row);
+		}
+		
+		// If |expand|, open row if container
+		if (expand && this.isContainer(row) && !this.isContainerOpen(row)) {
+			this.toggleOpenState(row);
+		}
 		this.selection.select(row);
 	}
-	else {
-		promise = this.waitForSelect();
-		this.selection.select(row);
+	// Ignore NS_ERROR_UNEXPECTED from nsITreeSelection::select(), apparently when the tree
+	// disappears before it's called (though I can't reproduce it):
+	//
+	// https://forums.zotero.org/discussion/comment/297039/#Comment_297039
+	catch (e) {
+		Zotero.logError(e);
 	}
 	
-	// If |expand|, open row if container
-	if (expand && this.isContainer(row) && !this.isContainerOpen(row)) {
-		this.toggleOpenState(row);
-	}
-	this.selection.select(row);
-	
 	if (promise) {
 		yield promise;
 	}
@@ -2143,30 +2119,40 @@ Zotero.ItemTreeView.prototype.rememberSelection = function (selection) {
 		var unsuppress = this.selection.selectEventsSuppressed = true;
 		this._treebox.beginUpdateBatch();
 	}
-	for(var i=0; i < selection.length; i++)
-	{
-		if (this._rowMap[selection[i]] != null) {
-			this.selection.toggleSelect(this._rowMap[selection[i]]);
-		}
-		// Try the parent
-		else {
-			var item = Zotero.Items.get(selection[i]);
-			if (!item) {
-				continue;
-			}
-			
-			var parent = item.parentItemID;
-			if (!parent) {
-				continue;
-			}
-			
-			if (this._rowMap[parent] != null) {
-				this._closeContainer(this._rowMap[parent]);
-				this.toggleOpenState(this._rowMap[parent]);
+	
+	try {
+		for (let i = 0; i < selection.length; i++) {
+			if (this._rowMap[selection[i]] != null) {
 				this.selection.toggleSelect(this._rowMap[selection[i]]);
 			}
+			// Try the parent
+			else {
+				var item = Zotero.Items.get(selection[i]);
+				if (!item) {
+					continue;
+				}
+				
+				var parent = item.parentItemID;
+				if (!parent) {
+					continue;
+				}
+				
+				if (this._rowMap[parent] != null) {
+					this._closeContainer(this._rowMap[parent]);
+					this.toggleOpenState(this._rowMap[parent]);
+					this.selection.toggleSelect(this._rowMap[selection[i]]);
+				}
+			}
 		}
 	}
+	// Ignore NS_ERROR_UNEXPECTED from nsITreeSelection::toggleSelect(), apparently when the tree
+	// disappears before it's called (though I can't reproduce it):
+	//
+	// https://forums.zotero.org/discussion/69226/papers-become-invisible-in-the-middle-pane
+	catch (e) {
+		Zotero.logError(e);
+	}
+	
 	if (unsuppress) {
 		this._treebox.endUpdateBatch();
 		this.selection.selectEventsSuppressed = false;
@@ -3232,9 +3218,7 @@ Zotero.ItemTreeView.prototype.drop = Zotero.Promise.coroutine(function* (row, or
 	else if (dataType == 'text/x-moz-url' || dataType == 'application/x-moz-file') {
 		// Disallow drop into read-only libraries
 		if (!collectionTreeRow.editable) {
-			var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-					   .getService(Components.interfaces.nsIWindowMediator);
-			var win = wm.getMostRecentWindow("navigator:browser");
+			let win = Services.wm.getMostRecentWindow("navigator:browser");
 			win.ZoteroPane.displayCannotEditLibraryMessage();
 			return;
 		}
@@ -3252,17 +3236,29 @@ Zotero.ItemTreeView.prototype.drop = Zotero.Promise.coroutine(function* (row, or
 			var parentCollectionID = collectionTreeRow.ref.id;
 		}
 		
+		let addedItems = [];
 		var notifierQueue = new Zotero.Notifier.Queue;
 		try {
+			// If there's a single file being added to a parent, automatic renaming is enabled,
+			// and there are no other non-HTML attachments, we'll rename the file as long as it's
+			// an allowed type. The dragged data could be a URL, so we don't yet know the file type.
+			// This should be kept in sync with ZoteroPane.addAttachmentFromDialog().
+			let renameIfAllowedType = false;
+			let parentItem;
+			if (parentItemID && data.length == 1 && Zotero.Prefs.get('autoRenameFiles')) {
+				parentItem = Zotero.Items.get(parentItemID);
+				if (!parentItem.numNonHTMLFileAttachments()) {
+					renameIfAllowedType = true;
+				}
+			}
+			
 			for (var i=0; i<data.length; i++) {
 				var file = data[i];
 				
 				if (dataType == 'text/x-moz-url') {
 					var url = data[i];
 					if (url.indexOf('file:///') == 0) {
-						var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-								   .getService(Components.interfaces.nsIWindowMediator);
-						var win = wm.getMostRecentWindow("navigator:browser");
+						let win = Services.wm.getMostRecentWindow("navigator:browser");
 						// If dragging currently loaded page, only convert to
 						// file if not an HTML document
 						if (win.content.location.href != url ||
@@ -3280,17 +3276,17 @@ Zotero.ItemTreeView.prototype.drop = Zotero.Promise.coroutine(function* (row, or
 					
 					// Still string, so remote URL
 					if (typeof file == 'string') {
+						let item;
 						if (parentItemID) {
 							if (!collectionTreeRow.filesEditable) {
-								var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-										   .getService(Components.interfaces.nsIWindowMediator);
-								var win = wm.getMostRecentWindow("navigator:browser");
+								let win = Services.wm.getMostRecentWindow("navigator:browser");
 								win.ZoteroPane.displayCannotEditLibraryFilesMessage();
 								return;
 							}
-							yield Zotero.Attachments.importFromURL({
+							item = yield Zotero.Attachments.importFromURL({
 								libraryID: targetLibraryID,
 								url,
+								renameIfAllowedType,
 								parentItemID,
 								saveOptions: {
 									notifierQueue
@@ -3298,10 +3294,11 @@ Zotero.ItemTreeView.prototype.drop = Zotero.Promise.coroutine(function* (row, or
 							});
 						}
 						else {
-							var wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-									   .getService(Components.interfaces.nsIWindowMediator);
-							var win = wm.getMostRecentWindow("navigator:browser");
-							win.ZoteroPane.addItemFromURL(url, 'temporaryPDFHack'); // TODO: don't do this
+							let win = Services.wm.getMostRecentWindow("navigator:browser");
+							item = yield win.ZoteroPane.addItemFromURL(url, 'temporaryPDFHack'); // TODO: don't do this
+						}
+						if (item) {
+							addedItems.push(item);
 						}
 						continue;
 					}
@@ -3309,8 +3306,38 @@ Zotero.ItemTreeView.prototype.drop = Zotero.Promise.coroutine(function* (row, or
 					// Otherwise file, so fall through
 				}
 				
+				file = file.path;
+				
+				// Rename file if it's an allowed type
+				let fileBaseName = false;
+				if (renameIfAllowedType) {
+					 fileBaseName = yield Zotero.Attachments.getRenamedFileBaseNameIfAllowedType(
+						parentItem, file
+					);
+				}
+				
+				let item;
 				if (dropEffect == 'link') {
-					yield Zotero.Attachments.linkFromFile({
+					// Rename linked file, with unique suffix if necessary
+					try {
+						if (fileBaseName) {
+							let ext = Zotero.File.getExtension(file);
+							let newName = yield Zotero.File.rename(
+								file,
+								fileBaseName + (ext ? '.' + ext : ''),
+								{
+									unique: true
+								}
+							);
+							// Update path in case the name was changed to be unique
+							file = OS.Path.join(OS.Path.dirname(file), newName);
+						}
+					}
+					catch (e) {
+						Zotero.logError(e);
+					}
+					
+					item = yield Zotero.Attachments.linkFromFile({
 						file,
 						parentItemID,
 						collections: parentCollectionID ? [parentCollectionID] : undefined,
@@ -3320,15 +3347,15 @@ Zotero.ItemTreeView.prototype.drop = Zotero.Promise.coroutine(function* (row, or
 					});
 				}
 				else {
-					if (file.leafName.endsWith(".lnk")) {
-						let wm = Components.classes["@mozilla.org/appshell/window-mediator;1"]
-						   .getService(Components.interfaces.nsIWindowMediator);
-						let win = wm.getMostRecentWindow("navigator:browser");
-						win.ZoteroPane.displayCannotAddShortcutMessage(file.path);
+					if (file.endsWith(".lnk")) {
+						let win = Services.wm.getMostRecentWindow("navigator:browser");
+						win.ZoteroPane.displayCannotAddShortcutMessage(file);
 						continue;
 					}
-					yield Zotero.Attachments.importFromFile({
+					
+					item = yield Zotero.Attachments.importFromFile({
 						file,
+						fileBaseName,
 						libraryID: targetLibraryID,
 						parentItemID,
 						collections: parentCollectionID ? [parentCollectionID] : undefined,
@@ -3339,18 +3366,27 @@ Zotero.ItemTreeView.prototype.drop = Zotero.Promise.coroutine(function* (row, or
 					// If moving, delete original file
 					if (dragData.dropEffect == 'move') {
 						try {
-							file.remove(false);
+							yield OS.File.remove(file);
 						}
 						catch (e) {
-							Components.utils.reportError("Error deleting original file " + file.path + " after drag");
+							Zotero.logError("Error deleting original file " + file + " after drag");
 						}
 					}
 				}
+				
+				if (item) {
+					addedItems.push(item);
+				}
 			}
 		}
 		finally {
 			yield Zotero.Notifier.commit(notifierQueue);
 		}
+		
+		// Automatically retrieve metadata for PDFs
+		if (!parentItemID) {
+			Zotero.RecognizePDF.autoRecognizeItems(addedItems);
+		}
 	}
 });
 

chrome/content/zotero/xpcom/mime.js

@@ -26,7 +26,6 @@
 Zotero.MIME = new function(){
 	this.isTextType = isTextType;
 	this.getPrimaryExtension = getPrimaryExtension;
-	this.sniffForMIMEType = sniffForMIMEType;
 	this.sniffForBinary = sniffForBinary;
 	this.hasNativeHandler = hasNativeHandler;
 	this.hasInternalHandler = hasInternalHandler;
@@ -48,8 +47,9 @@ Zotero.MIME = new function(){
 		["\uFFFDPNG", 'image/png', 0],
 		["JFIF", 'image/jpeg'],
 		["FLV", "video/x-flv", 0],
-		["\u0000\u0000\u0001\u0000", "image/vnd.microsoft.icon", 0]
-		
+		["\u0000\u0000\u0001\u0000", "image/vnd.microsoft.icon", 0],
+		["\u0053\u0051\u004C\u0069\u0074\u0065\u0020\u0066"
+			+ "\u006F\u0072\u006D\u0061\u0074\u0020\u0033\u0000", "application/x-sqlite3", 0]
 	];
 	
 	var _extensions = {
@@ -103,10 +103,6 @@ Zotero.MIME = new function(){
 	var _nativeMIMETypes = {
 		'text/html': true,
 		'text/css': true,
-		'image/jpeg': true,
-		'image/gif': true,
-		'image/png': true,
-		'image/svg+xml': true,
 		'text/xml': true,
 		'application/xhtml+xml': true,
 		'application/xml': true,
@@ -232,12 +228,12 @@ Zotero.MIME = new function(){
 	/*
 	 * Searches string for magic numbers
 	 */
-	function sniffForMIMEType(str){
-		for (var i in _snifferEntries){
-			var match = false;
+	this.sniffForMIMEType = function (str) {
+		for (let i in _snifferEntries) {
+			let match = false;
 			// If an offset is defined, match only from there
-			if (typeof _snifferEntries[i][2] != 'undefined') {
-				if (str.substr(i[2]).indexOf(_snifferEntries[i][0]) == 0) {
+			if (_snifferEntries[i][2] != undefined) {
+				if (str.substr(_snifferEntries[i][2]).indexOf(_snifferEntries[i][0]) == 0) {
 					match = true;
 				}
 			}
@@ -278,7 +274,7 @@ Zotero.MIME = new function(){
 	 * ext is an optional file extension hint if data sniffing is unsuccessful
 	 */
 	this.getMIMETypeFromData = function (str, ext){
-		var mimeType = sniffForMIMEType(str);
+		var mimeType = this.sniffForMIMEType(str);
 		if (mimeType){
 			Zotero.debug('Detected MIME type ' + mimeType);
 			return mimeType;

chrome/content/zotero/xpcom/notifier.js

@@ -32,7 +32,7 @@ Zotero.Notifier = new function(){
 		'collection-item', 'item-tag', 'tag', 'setting', 'group', 'trash',
 		'bucket', 'relation', 'feed', 'feedItem', 'sync', 'api-key'
 	];
-	var _inTransaction;
+	var _transactionID = false;
 	var _queue = {};
 
 
@@ -106,7 +106,7 @@ Zotero.Notifier = new function(){
 	* - New events and types should be added to the order arrays in commit()
 	**/
 	this.trigger = Zotero.Promise.coroutine(function* (event, type, ids, extraData, force) {
-		if (_inTransaction && !force) {
+		if (_transactionID && !force) {
 			return this.queue(event, type, ids, extraData);
 		}
 		
@@ -173,7 +173,7 @@ Zotero.Notifier = new function(){
 			queue = queue._queue;
 		}
 		else {
-			if (!_inTransaction) {
+			if (!_transactionID) {
 				throw new Error("Can't queue event outside of a transaction");
 			}
 			queue = _queue;
@@ -278,11 +278,11 @@ Zotero.Notifier = new function(){
 	 *
 	 * Note: Be sure the matching commit() gets called (e.g. in a finally{...} block) or
 	 * notifications will break until Firefox is restarted or commit(true)/reset() is called manually
+	 *
+	 * @param {String} [transactionID]
 	 */
-	this.begin = function () {
-		if (!_inTransaction) {
-			_inTransaction = true;
-		}
+	this.begin = function (transactionID = true) {
+		_transactionID = transactionID;
 	}
 	
 	
@@ -291,8 +291,9 @@ Zotero.Notifier = new function(){
 	 *
 	 * @param {Zotero.Notifier.Queue|Zotero.Notifier.Queue[]} [queues] - One or more queues to use
 	 *     instead of the internal queue
+	 * @param {String} [transactionID]
 	 */
-	this.commit = Zotero.Promise.coroutine(function* (queues) {
+	this.commit = Zotero.Promise.coroutine(function* (queues, transactionID = true) {
 		if (queues) {
 			if (!Array.isArray(queues)) {
 				queues = [queues];
@@ -308,7 +309,7 @@ Zotero.Notifier = new function(){
 				}
 			}
 		}
-		else if (!_inTransaction) {
+		else if (!_transactionID) {
 			throw new Error("Can't commit outside of transaction");
 		}
 		else {
@@ -375,7 +376,7 @@ Zotero.Notifier = new function(){
 		}
 		
 		if (!queues) {
-			this.reset();
+			this.reset(transactionID);
 		}
 		
 		if (totals) {
@@ -407,10 +408,13 @@ Zotero.Notifier = new function(){
 	/*
 	 * Reset the event queue
 	 */
-	this.reset = function () {
+	this.reset = function (transactionID = true) {
+		if (transactionID != _transactionID) {
+			return;
+		}
 		//Zotero.debug("Resetting notifier event queue");
 		_queue = {};
-		_inTransaction = false;
+		_transactionID = false;
 	}
 }
 

chrome/content/zotero/xpcom/openPDF.js

@@ -0,0 +1,287 @@
+/*
+    ***** BEGIN LICENSE BLOCK *****
+    
+    Copyright © 2018 Center for History and New Media
+                     George Mason University, Fairfax, Virginia, USA
+                     https://zotero.org
+    
+    This file is part of Zotero.
+    
+    Zotero is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    
+    Zotero is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+    
+    You should have received a copy of the GNU Affero General Public License
+    along with Zotero.  If not, see <http://www.gnu.org/licenses/>.
+    
+    ***** END LICENSE BLOCK *****
+*/
+
+Zotero.OpenPDF = {
+	openToPage: async function (path, page) {
+		var handler = Zotero.Prefs.get("fileHandler.pdf");
+		var opened = false;
+		if (Zotero.isMac) {
+			if (handler.includes('Preview')) {
+				this._openWithPreview(path, page);
+			}
+			else if (handler.includes('Skim')) {
+				this._openWithSkim(path, page);
+			}
+			else if (handler.includes('PDF Expert')) {
+				this._openWithPDFExpert(path, page);
+			}
+			else {
+				// Try to detect default app
+				handler = this._getPDFHandlerName();
+				Zotero.debug(`Handler is ${handler}`);
+				if (handler && handler == 'Skim') {
+					this._openWithSkim(path, page);
+				}
+				else if (handler && handler == 'PDF Expert') {
+					this._openWithPDFExpert(path, page);
+				}
+				// Fall back to Preview
+				else {
+					this._openWithPreview(path, page);
+				}
+			}
+			opened = true;
+		}
+		else if (Zotero.isWin) {
+			handler = handler || this._getPDFHandlerWindows();
+			// Include flags to open the PDF on a given page in various apps
+			//
+			// Adobe Acrobat: http://partners.adobe.com/public/developer/en/acrobat/PDFOpenParameters.pdf
+			// PDF-XChange: http://help.tracker-software.com/eu/default.aspx?pageid=PDFXView25:command_line_options
+			let args = ['/A', 'page=' + page, path];
+			Zotero.Utilities.Internal.exec(handler, args);
+			opened = true;
+		}
+		else if (Zotero.isLinux) {
+			if (handler.includes('evince') || handler.includes('okular')) {
+				this._openWithEvinceOrOkular(handler, path, page);
+				opened = true;
+			}
+			else {
+				let handler = await this._getPDFHandlerLinux();
+				if (handler.includes('evince') || handler.includes('okular')) {
+					this._openWithEvinceOrOkular(handler, path, page);
+					opened = true;
+				}
+				// Fall back to okular and then evince if unknown handler
+				else if (await OS.File.exists('/usr/bin/okular')) {
+					this._openWithEvinceOrOkular('/usr/bin/okular', path, page);
+					opened = true;
+				}
+				else if (await OS.File.exists('/usr/bin/evince')) {
+					this._openWithEvinceOrOkular('/usr/bin/evince', path, page);
+					opened = true;
+				}
+				else {
+					Zotero.debug("No handler found");
+				}
+			}
+		}
+		return opened;
+	},
+	
+	_getPDFHandlerName: function () {
+		var handlerService = Cc["@mozilla.org/uriloader/handler-service;1"]
+			.getService(Ci.nsIHandlerService);
+		var handlers = handlerService.enumerate();
+		var handler;
+		while (handlers.hasMoreElements()) {
+			let handlerInfo = handlers.getNext().QueryInterface(Ci.nsIHandlerInfo);
+			if (handlerInfo.type == 'application/pdf') {
+				handler = handlerInfo;
+				break;
+			}
+		}
+		if (!handler) {
+			// We can't get the name of the system default handler unless we add an entry
+			Zotero.debug("Default handler not found -- adding default entry");
+			let mimeService = Components.classes["@mozilla.org/mime;1"]
+				.getService(Components.interfaces.nsIMIMEService);
+			let mimeInfo = mimeService.getFromTypeAndExtension("application/pdf", "");
+			mimeInfo.preferredAction = 4;
+			mimeInfo.alwaysAskBeforeHandling = false;
+			handlerService.store(mimeInfo);
+			
+			// And once we do that, we can get the name (but not the path, unfortunately)
+			let handlers = handlerService.enumerate();
+			while (handlers.hasMoreElements()) {
+				let handlerInfo = handlers.getNext().QueryInterface(Ci.nsIHandlerInfo);
+				if (handlerInfo.type == 'application/pdf') {
+					handler = handlerInfo;
+					break;
+				}
+			}
+		}
+		if (handler) {
+			Zotero.debug(`Default handler is ${handler.defaultDescription}`);
+			return handler.defaultDescription;
+		}
+		return false;
+	},
+	
+	//
+	// Mac
+	//
+	_openWithPreview: async function (filePath, page) {
+		await Zotero.Utilities.Internal.exec('/usr/bin/open', ['-a', 'Preview', filePath]);
+		// Go to page using AppleScript
+		let args = [
+			'-e', 'tell app "Preview" to activate',
+			'-e', 'tell app "System Events" to keystroke "g" using {option down, command down}',
+			'-e', `tell app "System Events" to keystroke "${page}"`,
+			'-e', 'tell app "System Events" to keystroke return'
+		];
+		await Zotero.Utilities.Internal.exec('/usr/bin/osascript', args);
+	},
+	
+	_openWithSkim: async function (filePath, page) {
+		// Escape double-quotes in path
+		var quoteRE = /"/g;
+		filePath = filePath.replace(quoteRE, '\\"');
+		let filename = OS.Path.basename(filePath).replace(quoteRE, '\\"');
+		let args = [
+			'-e', 'tell app "Skim" to activate',
+			'-e', `tell app "Skim" to open "${filePath}"`
+		];
+		args.push('-e', `tell document "${filename}" of application "Skim" to go to page ${page}`);
+		await Zotero.Utilities.Internal.exec('/usr/bin/osascript', args);
+	},
+	
+	_openWithPDFExpert: async function (filePath, page) {
+		await Zotero.Utilities.Internal.exec('/usr/bin/open', ['-a', 'PDF Expert', filePath]);
+		// Go to page using AppleScript (same as Preview)
+		let args = [
+			'-e', 'tell app "PDF Expert" to activate',
+			'-e', 'tell app "System Events" to keystroke "g" using {option down, command down}',
+			'-e', `tell app "System Events" to keystroke "${page}"`,
+			'-e', 'tell app "System Events" to keystroke return'
+		];
+		await Zotero.Utilities.Internal.exec('/usr/bin/osascript', args);
+	},
+	
+	//
+	// Windows
+	//
+	/**
+	 * Get path to default pdf reader application on windows
+	 * @return {string} Path to default pdf reader application
+	 *
+	 * From getPDFReader() in ZotFile (GPL)
+	 * https://github.com/jlegewie/zotfile/blob/master/chrome/content/zotfile/utils.js
+	 */
+	_getPDFHandlerWindows: function () {
+		var wrk = Components.classes["@mozilla.org/windows-registry-key;1"]
+			.createInstance(Components.interfaces.nsIWindowsRegKey);
+		// Get handler for PDFs
+		var tryKeys = [
+			{
+				root: wrk.ROOT_KEY_CURRENT_USER,
+				path: 'Software\\Microsoft\\Windows\\CurrentVersion\\Explorer\\FileExts\\.pdf\\UserChoice',
+				value: 'Progid'
+			},
+			{
+				root: wrk.ROOT_KEY_CLASSES_ROOT,
+				path: '.pdf',
+				value: ''
+			}
+		];
+		var progId;
+		for (let i = 0; !progId && i < tryKeys.length; i++) {
+			try {
+				wrk.open(
+					tryKeys[i].root,
+					tryKeys[i].path,
+					wrk.ACCESS_READ
+				);
+				progId = wrk.readStringValue(tryKeys[i].value);
+			}
+			catch (e) {}
+		}
+		
+		if (!progId) {
+			wrk.close();
+			return;
+		}
+		
+		// Get version specific handler, if it exists
+		try {
+			wrk.open(
+				wrk.ROOT_KEY_CLASSES_ROOT,
+				progId + '\\CurVer',
+				wrk.ACCESS_READ
+			);
+			progId = wrk.readStringValue('') || progId;
+		}
+		catch (e) {}
+		
+		// Get command
+		var success = false;
+		tryKeys = [
+			progId + '\\shell\\Read\\command',
+			progId + '\\shell\\Open\\command'
+		];
+		for (let i = 0; !success && i < tryKeys.length; i++) {
+			try {
+				wrk.open(
+					wrk.ROOT_KEY_CLASSES_ROOT,
+					tryKeys[i],
+					wrk.ACCESS_READ
+				);
+				success = true;
+			}
+			catch (e) {}
+		}
+		
+		if (!success) {
+			wrk.close();
+			return;
+		}
+		
+		var command = wrk.readStringValue('').match(/^(?:".+?"|[^"]\S+)/);
+		
+		wrk.close();
+		
+		if (!command) return;
+		return command[0].replace(/"/g, '');
+	},
+	
+	//
+	// Linux
+	//
+	_getPDFHandlerLinux: async function () {
+		var name = this._getPDFHandlerName();
+		switch (name.toLowerCase()) {
+		case 'okular':
+			return `/usr/bin/${name}`;
+		
+		// It's "Document Viewer" on stock Ubuntu
+		case 'document viewer':
+		case 'evince':
+			return `/usr/bin/evince`;
+		}
+		
+		// TODO: Try to get default from mimeapps.list, etc., in case system default is okular
+		// or evince somewhere other than /usr/bin
+		var homeDir = OS.Constants.Path.homeDir;
+		
+		return false;
+		
+	},
+	
+	_openWithEvinceOrOkular: function (appPath, filePath, page) {
+		var args = ['-p', page, filePath];
+		Zotero.Utilities.Internal.exec(appPath, args);
+	}
+}

chrome/content/zotero/xpcom/profile.js

@@ -70,8 +70,17 @@ Zotero.Profile = {
 			? OS.Path.join(profilesDir, ...defaultSection.Path.split("/"))
 			: defaultSection.Path;
 		
-		if (!(yield OS.File.exists(defaultProfile))) {
-			return false;
+		try {
+			// Note: exists() returns false on no access, so use stat() instead
+			yield OS.File.stat(defaultProfile);
+		}
+		catch (e) {
+			if (e instanceof OS.File.Error) {
+				if (e.becauseNoSuchFile) {
+					return false;
+				}
+				throw e;
+			}
 		}
 		return [defaultProfile, nSections > 1];
 	}),
@@ -120,10 +129,12 @@ Zotero.Profile = {
 	/**
 	 * Find other profile directories (for this app or the other app) using the given data directory
 	 *
+	 * @param {String} dataDir
+	 * @param {Boolean} [includeOtherApps=false] - Check Firefox profiles
 	 * @return {String[]}
 	 */
-	findOtherProfilesUsingDataDirectory: Zotero.Promise.coroutine(function* (dataDir) {
-		let otherAppProfiles = yield this._findOtherAppProfiles();
+	findOtherProfilesUsingDataDirectory: Zotero.Promise.coroutine(function* (dataDir, includeOtherApps = true) {
+		let otherAppProfiles = includeOtherApps ? (yield this._findOtherAppProfiles()) : [];
 		let otherProfiles = (yield this._findOtherProfiles()).concat(otherAppProfiles);
 		
 		// First get profiles pointing at this directory
@@ -189,6 +200,78 @@ Zotero.Profile = {
 	}),
 	
 	
+	/**
+	 * @return {Boolean} - True if accessible or skipped, false if not
+	 */
+	checkFirefoxProfileAccess: async function () {
+		try {
+			let profilesParent = OS.Path.dirname(Zotero.Profile.getOtherAppProfilesDir());
+			Zotero.debug("Looking for Firefox profile in " + profilesParent);
+			let defProfile = await this.getDefaultInProfilesDir(profilesParent);
+			if (defProfile) {
+				let profileDir = defProfile[0];
+				Zotero.debug("Found default profile at " + profileDir);
+				let prefsFile = OS.Path.join(profileDir, "prefs.js");
+				await Zotero.File.getContentsAsync(prefsFile);
+				let dir = OS.Path.join(profileDir, Zotero.DataDirectory.legacyDirName);
+				Zotero.debug("Checking for 'zotero' subdirectory");
+				if ((await OS.File.stat(dir)).isDir) {
+					let dbFilename = Zotero.DataDirectory.getDatabaseFilename();
+					let dbFile = OS.Path.join(dir, dbFilename);
+					Zotero.debug("Checking database access within 'zotero' subdirectory");
+					(await OS.File.stat(dbFile)).lastModificationDate;
+				}
+				else {
+					Zotero.debug("'zotero' is not a directory!");
+				}
+			}
+			else {
+				Zotero.debug("No default profile found");
+			}
+		}
+		catch (e) {
+			if (e instanceof OS.File.Error && e.becauseNoSuchFile) {
+				return true;
+			}
+			Zotero.debug(e, 2)
+			return false
+		}
+		return true;
+	},
+	
+	
+	readPrefsFromFile: async function (prefsFile) {
+		var sandbox = new Components.utils.Sandbox("http://www.example.com/");
+		Components.utils.evalInSandbox(
+			"var prefs = {};"+
+			"function user_pref(key, val) {"+
+				"prefs[key] = val;"+
+			"}"
+		, sandbox);
+		
+		(await Zotero.File.getContentsAsync(prefsFile))
+			.split(/\n/)
+			.filter((line) => {
+				// Strip comments
+				return !line.startsWith('#')
+					// Only process lines in our pref branch
+					&& line.includes(ZOTERO_CONFIG.PREF_BRANCH);
+			})
+			// Process each line individually
+			.forEach((line) => {
+				try {
+					Zotero.debug("Processing " + line);
+					Components.utils.evalInSandbox(line, sandbox);
+				}
+				catch (e) {
+					Zotero.logError("Error processing prefs line: " + line);
+				}
+			});
+		
+		return sandbox.prefs;
+	},
+	
+	
 	//
 	// Private methods
 	//

chrome/content/zotero/xpcom/progressWindow.js

@@ -154,6 +154,9 @@ Zotero.ProgressWindow = function(options = {}) {
 		_progressWindow.addEventListener("mouseover", _onMouseOver, false);
 		_progressWindow.addEventListener("mouseout", _onMouseOut, false);
 		_progressWindow.addEventListener("mouseup", _onMouseUp, false);
+		_window.addEventListener('close', () => {
+			this.close();
+		});
 		
 		_windowLoading = true;
 		
@@ -281,7 +284,10 @@ Zotero.ProgressWindow = function(options = {}) {
 		
 		try {
 			_progressWindow.close();
-		} catch(ex) {}
+		}
+		catch (e) {
+			Zotero.logError(e);
+		}
 	}
 	
 	/**

chrome/content/zotero/xpcom/proxy.js

@@ -321,7 +321,11 @@ Zotero.Proxy.prototype.compileRegexp = function() {
 	})
 	
 	// now replace with regexp fragment in reverse order
-	var re = "^"+Zotero.Utilities.quotemeta(this.scheme)+"$";
+	if (this.scheme.includes('://')) {
+		re = "^"+Zotero.Utilities.quotemeta(this.scheme)+"$";
+	} else {
+		re = "^https?"+Zotero.Utilities.quotemeta('://'+this.scheme)+"$";
+	}
 	for(var i=this.parameters.length-1; i>=0; i--) {
 		var param = this.parameters[i];
 		re = re.replace(Zotero_Proxy_schemeParameterRegexps[param], "$1"+parametersToCheck[param]);