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-implementer-prompt.txt

@@ -14,6 +14,7 @@ Full access: read, write, edit, delete, bash, grep, glob, git_operator, lsp_*, s
 6. Run `cargo build` or equivalent after each logical chunk.
 7. If you encounter an issue not covered by the plan, use `note_finding` to flag it.
 8. Update todo.md as you complete each file: `todofinish`
+9. NEVER use 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 skip or silence warnings. Fix the underlying code to adhere to linter guidelines.
 
 ## Output
 After each file: confirm what was implemented and any deviations from plan.