Refactor storage layer abstraction

Would like to do the following:
- Ability to drop-in a replacement for Sqlite in order to support people bringing their own DB. Ideally in such a way that no changes are required to application logic after adding support.

Start by locating the storage layer and its SQLite integration in the repository, then trace how application logic accesses persistence. Identify the boundaries a replacement database would need to implement and review whether the issue needs a more specific design before coding. Done means an alternative database can be supported without application-logic changes.

Written by the indexing model from the issue text.