Refactor simplify()

Use a logic similar to manifests, but internal to the commit. This should be much faster than doing as many O(n^2) passes as needed for the result to be invariant.

It actually fixed a bug where an M followed by a D were both deleted, but the D must stay because maybe the M overwrote an already existing file, which would leak through if the D was removed too. See the changes in the restructure.chk test.