Fixed bug where changes to the package could not be seen after update (#894)

Actually there were two bugs, both related to the fact that we now keep files in
OPAMROOT/packages for uninstalled packages (the update in OPAMROOT/repo/... was ok):

* the package state was not looked up there when the package was not
installed, instead looking in the repo dir (which was already updated)
and concluded that no modifications were made

* the uninstalled packages were not kept in the set of changed
packages, and not updated by
OpamRepositoryCommand.fix_package_descriptions

fix_package_descriptions now removes such obsolete files if the package is installed
nowhere, since there is little point in keeping them up-to-date forever.