feat(mcp): implement persistent codebase status and info retrieval from file

[IvanM9]

This pull request improves the reliability and consistency of codebase status and information retrieval in the SnapshotManager class by reading from the persisted JSON snapshot file instead of relying solely on in-memory data. The changes also add compatibility for both v1 and v2 snapshot formats and introduce robust error handling.

Persistence and consistency improvements:

• Updated getCodebaseStatus to read codebase status from the JSON snapshot file, ensuring results reflect the persisted state and supporting both v1 and v2 formats. If file reading fails, it falls back to in-memory data.
• Updated getCodebaseInfo to retrieve complete codebase information from the JSON snapshot file, constructing results for v1 format and supporting v2 format directly. Falls back to in-memory data on error.

Backward compatibility and error handling:

• Added logic to handle both v1 and v2 formats for indexed and indexing codebases, including handling array and object formats for indexing codebases.
• Added error handling and logging to warn if reading from the snapshot file fails, ensuring graceful fallback to in-memory data.