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.
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