Refactor configuration dict into CompilationDatabase

[Pennycook]

Feature/behavior summary

The configuration dictionary used by Code Base Investigator 1.x stores a subset of the information available in a compilation database. Rather than maintain support for two data formats and move back and forth between them, we should adopt compilation databases as the only representation of a compilation.

Request attributes

• [X] Would this be a refactor of existing code?
• [ ] Does this proposal require new package dependencies?
• [X] Would this change break backwards compatibility?

Related issues

No response

Solution description

• Introduce a CompilationDatabase class that stores CompileCommand objects and is interoperable with JSON.
• Rewrite external interface(s) to use a CompilationDatabase and update the tests.
• Rewrite internal interface(s) to use a CompilationDatabase (replacing functionality from config.py).

Additional notes

No response