Merge LDBStore `CleanIndex` with `Cleanup`

[frncmx]

Created from #976

Let's postpone the merging of 2 complicated functions until:
A) We rewrite the storage (Do we have an open issue on this?)
B) We introduce a dirty bit to the DB (Reference an issue here?), so that we know we have to check our index let's say after an unclean shutdown.

Note: Currently CleanIndex is super slow (can take hours). Maybe we could optimize by only looking for inconsistent entries and drop only those in contrast to rebuilding the whole index from scratch.

[frncmx]

@nolash what do you think? Did I manage to capture what we discussed?