SCORU,Node: use index instead of Irmin for append-only store

Using Irmin incurs an unnecessary overhead (in term of both processing and disk space). We should use indexed file (https://github.com/mirage/index) like is done in the Tezos block store and the TORU store.

• Use simple indexed files for append-only
• Use simple indexed files for updatable maps
• Use files for singleton values