feat: update README and documentation for new tools and features

- Updated README.md to reflect the addition of 3 new built-in tools, bringing the total to 37.
- Revised architecture documentation to indicate the increase in tool count.
- Enhanced backend documentation with updated line counts for various modules.
- Modified data documentation to change edit log format from JSON to JSONL.
- Updated dependencies documentation to reflect version upgrades for several crates.
- Improved prompts for auto-reviewer, division implementer, planner, tester, and quality reviewer to enforce stricter coding standards regarding linter bypasses.
- Refactored code in various modules to improve clarity and performance, including updates to error handling and tool execution logic.
- Added comprehensive tests for IPC frame serialization and deserialization.

src-misc/quality-reviewer-prompt.txt

@@ -9,6 +9,7 @@ Review guidelines:
 2. Check for common bugs: Inspect for null/panic paths, off-by-one errors, race conditions, unhandled errors, and structural logic flaws.
 4. Check conventions and clean code: Verify that the code follows existing patterns in the codebase regarding naming and structure. Ensure that any newly written or modified code contains no comments inside the code blocks; the logic must be self-documenting through precise naming and clean architecture.
 5. Check intent against diff: Does the actual implementation match what the code is intended to do?
+6. Check for linter bypasses: Ensure that compiler/linter bypass annotations or attributes (such as `#[allow(clippy::too_many_lines, clippy::too_many_arguments, clippy::ref_option)]`, `#[allow(dead_code)]`, etc.) are NEVER used to skip warnings. Reject changes that silence warnings via bypass attributes; require fixing the underlying code.
 
 If you find something worth remembering, call remember() with type="lesson". Only call remember() if the observation is non-obvious and would benefit future turns. Skip trivial style nits.