# Implementation Plan: Codebase Audit and Cleanup

## Phase 1: Audit and Refactor Orchestration & DAG Core [checkpoint: db03a78]
- [x] Task: Audit `src/multi_agent_conductor.py` for redundant logic, missing docstrings, and organization. 373f4ed
    - [ ] Perform minor refactoring of small redundancies.
    - [ ] Add minimal docstrings to critical paths.
    - [ ] Document large architectural redundancies if found.
- [x] Task: Audit `src/dag_engine.py` for redundant logic, missing docstrings, and organization. f11a219
    - [ ] Perform minor refactoring of small redundancies.
    - [ ] Add minimal docstrings to critical paths.
    - [ ] Document large architectural redundancies if found.
- [x] Task: Audit `src/native_orchestrator.py` and `src/orchestrator_pm.py`. 48abdc9
    - [ ] Perform minor refactoring of small redundancies.
    - [ ] Add minimal docstrings to critical paths.
    - [ ] Document large architectural redundancies if found.
- [x] Task: Conductor - User Manual Verification 'Phase 1: Audit and Refactor Orchestration & DAG Core' (Protocol in workflow.md)

## Phase 2: Audit and Refactor AI Clients & Tools [checkpoint: 27bcfb3]
- [x] Task: Audit `src/ai_client.py` and `src/gemini_cli_adapter.py`. 29dd6ec
    - [ ] Perform minor refactoring of small redundancies.
    - [ ] Add minimal docstrings to critical paths.
    - [ ] Document large architectural redundancies if found.
- [x] Task: Audit `src/mcp_client.py` and `src/shell_runner.py`. 6dd9b67
    - [ ] Perform minor refactoring of small redundancies.
    - [ ] Add minimal docstrings to critical paths.
    - [ ] Document large architectural redundancies if found.
- [x] Task: Audit `src/api_hook_client.py` and `src/api_hooks.py`. f9b5acd
    - [ ] Perform minor refactoring of small redundancies.
    - [ ] Add minimal docstrings to critical paths.
    - [ ] Document large architectural redundancies if found.
- [x] Task: Conductor - User Manual Verification 'Phase 2: Audit and Refactor AI Clients & Tools' (Protocol in workflow.md)

## Phase 3: Final Review and Reporting [checkpoint: 7e30a31]
- [x] Task: Compile findings of large architectural redundancies from Phase 1 and 2. 8364070
    - [ ] Generate a markdown report summarizing the findings.
- [x] Task: Conductor - User Manual Verification 'Phase 3: Final Review and Reporting' (Protocol in workflow.md)