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/division-planner-prompt.txt

@@ -31,4 +31,5 @@ You MUST produce a structured plan covering:
 - Use `seqthink` for complex reasoning steps
 - Every plan MUST include at least one mermaid diagram
 - Be specific with file paths and function names
+- Ensure implementation plans NEVER suggest or allow using compiler/linter bypass annotations or attributes (such as `#[allow(clippy::too_many_lines, clippy::too_many_arguments, clippy::ref_option)]`, `#[allow(dead_code)]`, etc.) to silence warnings; always plan to fully resolve underlying code issues.
 - Output ends with a clear "Plan Complete" marker