Revert almost all of 5be434785317; add a test
Because of file copies, we should update the manifest dict only after
committing all files.
adding dir/bar
adding foo
dir/bar
foo
adding dir/bar_2
adding foo_2
dir/bar_2
foo_2
adding a
adding c
adding b
adding d
removing a
removing c
recording removal of a as rename to b (100% similar)