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.

CLAUDE.md

@@ -37,7 +37,7 @@ Tracing output goes to `~/.local/share/zesdex/zesdex.log`. Set `RUST_LOG=debug`
 
 ## Architecture Overview
 
-Zesdex is an autonomous AI coding agent with a TUI — an OpenAI/Anthropic-compatible LLM client wrapped in a tool-use harness with 28 built-in tools.
+Zesdex is an autonomous AI coding agent with a TUI — an OpenAI/Anthropic-compatible LLM client wrapped in a tool-use harness with 37 built-in tools.
 
 Detailed architecture documentation is in `docs/CODEMAPS/`:
 
@@ -62,7 +62,7 @@ Detailed architecture documentation is in `docs/CODEMAPS/`:
 Controller (key input → Action) → Event Loop → LLM stream → Tool execution → State mutation → TUI render
   │                              │                              │
   │ src/controller/input.rs      │ src/app/runtime/actions/     │ src/tool/
-  └── maps keys to Action enum   │── dispatches Action::*      └── 28 tool impls
+  └── maps keys to Action enum   │── dispatches Action::*      └── 37 tool impls
                                  │    matching on Action variant
                                  │── applies state mutations
 ```
@@ -167,3 +167,4 @@ Rules:
 - Non-trivial private functions (≥10 lines) need a doc comment
 - Write the comment above the code it documents (not inline in the body)
 - Update comments when code behavior changes — stale docs are worse than no docs
+- 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 silence warnings or skip linter checks. Always fix the underlying code issues instead.