Revert bogus optimization that avoids index file writes

Revert bogus optimization that avoids index file writes

It didn't properly mark all cache updates as being dirty, and
causes merge errors due to that. In particular, it didn't notice
when a file was force-removed.

Besides, it was ugly as hell. I've put in place a slightly cleaner
version, but I've not enabled the optimization because I don't
want to be burned again.