Persistence Layer Refactor

Localize the state for updating everything related to the the store. Now each part of the database that is updated is a self contained stage. Events flow through the stages constructing actions that are applied atomically. This PR should be semantically identically except for a couple bug fixes. This is part of progress of making polycentric-core more generic for different use cases. Different applications may want to index different things. In general this refactor also makes things cleaner.