get rid of need to run pre-commit hook when assistant commits in direct mode

That hook updates associated file bookkeeping info for direct mode.
But, everything already called addAssociatedFile when adding/changing a
file. It only needed to also call removeAssociatedFile when deleting a file,
or a directory.

This should make bulk adds faster, by some possibly significant amount.
Bulk removals may be a little slower, since it has to use catKeyFile now
on each removed file, but will still be faster than adds.

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