codeintel: Collapse layer of abstraction in lsifstore

Created by: efritz

The current lsifstore package began its life as the bundle manager API. This separation is still apparent in the implementation: there was the distinct backend that operated over a single SQLite dump (the contents of data_read.go), and an API layer that translated the results (the contents of bundle.go). This PR collapses that abstraction so that the public API methods query the underlying datastore directly.

This is a refactoring pre-step to https://github.com/sourcegraph/sourcegraph/issues/15945, which will include a similar boundary collapse between some subset of {lsifstore, codeintel api, codeintel resolvers}.