Use nonrelative paths instead of absolute paths for cloned repositories

Use nonrelative paths instead of absolute paths for cloned repositories

Particularly for the "alternates" file, if one will be created, we
want a path that doesn't depend on the current directory, but we want
to retain any symlinks in the path as given and any in the user's view
of the current directory when the path was given.

Signed-off-by: Daniel Barkalow <barkalow@iabervon.org>
Signed-off-by: Junio C Hamano <gitster@pobox.com>