Memory usage is at its highest during cleanup

[fingon]

The sqlite approach should be probably adapted to it too - keep track of the files that are in use there, instead of keeping (millions of) Python strings in memory. FYI @joelynch

#161 fixes this somewhat (keep only manifests that are actually active, not historic ones, in memory) but we should really split the manifest to per-node sub-manifests with file references.