This change refactors all direct JSON file writes to use the safeWriteJson
utility, which implements atomic file writes to prevent data corruption
during write operations.

- Modified safeWriteJson to accept optional replacer and space arguments
- Updated tests to verify correct behavior with the new implementation

Fixes: #722
Signed-off-by: Eric Wheeler <[email protected]>

Replaces the previous in-memory lock in `safeWriteJson` with
`proper-lockfile` to provide robust, cross-process advisory file
locking. This enhances safety when multiple processes might attempt
concurrent writes to the same JSON file.

Key changes:
- Added `proper-lockfile` and `@types/proper-lockfile` dependencies.
- `safeWriteJson` now uses `proper-lockfile.lock()` with configured
  retries, staleness checks (31s), and lock update intervals (10s).
- An `onCompromised` handler is included to manage scenarios where
  the lock state is unexpectedly altered.
- Logging and comments within `safeWriteJson` have been refined for
  clarity, ensuring error logs include backtraces.
- The test suite `safeWriteJson.test.ts` has been significantly
  updated to:
    - Use real timers (`jest.useRealTimers()`).
    - Employ a more comprehensive mock for `fs/promises`.
    - Correctly manage file pre-existence for various scenarios.
    - Simulate lock contention by mocking `proper-lockfile.lock()`
      using `jest.doMock` and a dynamic require for the SUT.
    - Verify lock release by checking for the absence of the `.lock`
      file.

All tests are passing with these changes.

Signed-off-by: Eric Wheeler <[email protected]>

Refactor safeWriteJson to use stream-json for memory-efficient JSON serialization:
- Replace in-memory string creation with streaming pipeline
- Add Disassembler and Stringer from stream-json library
- Extract streaming logic to a dedicated helper function
- Add proper-lockfile and stream-json dependencies

This implementation reduces memory usage when writing large JSON objects.

Signed-off-by: Eric Wheeler <[email protected]>

- Use file path itself for locking instead of separate lock file
- Improve error handling and clarity of code
- Enhance cleanup of temporary files

Signed-off-by: Eric Wheeler <[email protected]>

- Ensure test file exists before locking
- Add proper mocking for fs.createWriteStream
- Fix test assertions to match expected behavior
- Improve test comments to follow project guidelines

Signed-off-by: Eric Wheeler <[email protected]>

Updated tests to work with safeWriteJson instead of direct fs.writeFile calls:

- Updated importExport.test.ts to expect safeWriteJson calls instead of fs.writeFile
- Fixed McpHub.test.ts by properly mocking fs/promises module:
  - Moved jest.mock() to the top of the file before any imports
  - Added mock implementations for all fs functions used by safeWriteJson
  - Updated the test setup to work with the mocked fs module

All tests now pass successfully.

Signed-off-by: Eric Wheeler <[email protected]>

Replace all non-test instances of JSON.stringify used for writing to JSON files with safeWriteJson to ensure safer file operations with proper locking, error handling, and atomic writes.

- Updated src/services/mcp/McpHub.ts
- Updated src/services/code-index/cache-manager.ts
- Updated src/api/providers/fetchers/modelEndpointCache.ts
- Updated src/api/providers/fetchers/modelCache.ts
- Updated tests to match the new implementation

Signed-off-by: Eric Wheeler <[email protected]>