magit-list-repos*: bugfix

Fix a bug introduced in 482de8051cbb0bba6e9f6bd533097cc7bbdeb7ad.
magit-list-repos*: ignore hidden files
improve magit-read-top-dir and its minions

* make `magit-list-repos' useful on its own
* rename `magit-list-repos-remove-conflicts' to
  magit-list-repos-uniquify'
* when uniquifying, _append_ containing directories
* ignore hidden directories
* cleanup