fix: backport stable hardening guards

[iLevyTate]

This pull request primarily focuses on backporting essential stability and hardening guards to core backend services and IPC handlers. The changes prevent potential memory leaks, address edge cases with late or missing responses, and ensure configuration settings are strictly respected.

Core services and IPC hardening:

• Hardened the chatIpc service by introducing a cleanup state to safely ignore late stream responses and prevent memory leaks.
• Updated the ParallelEmbeddingService to correctly preserve explicit zero-valued retry configurations by implementing nullish coalescing.
• Enhanced AtomicFileOperations to ensure transaction timeout timers are properly cleared upon transaction failure or rollback.
• Improved the auto-organize fileProcessor to safely handle missing suggestion payloads by utilizing optional chaining.

Testing and edge case coverage:

• Added comprehensive tests to chatIpc.test.js to verify that late query failures are ignored after cleanup and that malformed bridge responses are handled gracefully.
• Expanded edge case testing for the auto-organize fileProcessor to ensure files are correctly routed to the default folder when suggestion payloads are missing.
• Introduced new unit tests for the ParallelEmbeddingService to explicitly verify that zero-retry options are accurately preserved.