Update graph on edits

[vinistock]

Motivation

Start updating the graph when incremental edits happen. This PR handles both in-memory modifications (textDocument/didChange) and changes committed to disk (workspace/didChangeWatchedFiles).

Implementation

Some key decisions:

1. Incremental indexing and resolution now happens immediately for in-memory edits. We received feedback from several users that not every editor fires all feature requests and so attaching indexing to them is not adequate (Improve indexing behaviour (for editors other than VS Code, e.g. Zed) #3384). Additionally, Rubydex incremental indexing and resolution should be fast enough that we can do it every time
2. I removed Store#push_edits. That method didn't add much and I needed the document instance to access the source after modifications
3. Watched file notifications always send a string URI for the change[:uri], so I ensured all of our tests accurately reflected that