When a package "p" is clone-linked and the repo for "p" changes to be
a multi-package repository (e.g., with "p-lib", "p-doc", and "p"), a
`raco update` would get confused. Unofrtunately, a plain `raco pkg
update p` can't work in that case, because the clone link would still
be a pathless repo URL; the repairs make `raco pkg update --lookup
--clone ..../p` work as is should.
Related: fix inference of package names in the early check for whether
a package is installed.
If the clone directory's checkout includes a target commit, then
use the clone directory directly for staging (i.e., for checking
dependencies and collisions). That way, changes made locally are
used for metadata checks.
