Add index API to remove all files in a directory

This adds the git_index_remove_directory API plus tests.
Fix checkout of index-only dirs and prefixed paths

There are a couple of checkout bugs fixed here.  One is with
untracked working directory entries that are prefixes of tree
entries but not in a meaningful way (i.e. "read" is a prefix of
"readme.txt" but doesn't interfere in any way).  The second bug
is actually a redo of 07edfa0fc640f85f95507c3101e77accd7d2bf0d
where directory entries in the index that are not in the diff
were not being removed correctly.  That fix remedied one case
but broke another.