Symlink fixes

This fixes a few issues where the host filesystem might (slightly) influence builds due to symlinks. This also allows simplifying the CasBasedDirectory code a bit as it no longer has to match the previously odd behavior of list_relative_paths().

NOTE: This also removes the list_dirs parameter from list_relative_paths(), which is public API. There was a bug in that code path and I'm not aware of any users. I expect this to be acceptable for master but this should not be backported to 1.2.