fix(core): don't create a new project when the configuration changes

[ematipico]

Summary

Closes #3577

The bug: a new project was always created when a configuration was updated.

The fix

• we check if the project we registering is new or not. If not, we return the current key
• we don't throw an error if the manifest isn't found

I took the opportunity to do some minor refactors:

• more trace logging
• print the error in there's a failure inside the LSP

Test Plan

I tested it manually, as I was able to reproduce it locally. Now bug is gone and the Biome LSP doesn't crush anymore

[Conaclos]

A test is failing