prep doc track.

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# Implementation Plan: Documentation Refresh and Context Cleanup
This plan follows the project's standard task workflow to modernize documentation and decommission redundant context files.
## Phase 1: Context Cleanup
Permanently remove redundant files and update project-wide references.
# Implementation Plan: Deep Architectural Documentation Refresh
## Phase 1: Context Cleanup & Research
- [ ] Task: Audit references to `MainContext.md` across the project.
- [ ] Task: Write failing test that verifies the absence of `MainContext.md` and related broken links.
- [ ] Task: Delete `MainContext.md` and update any identified references.
- [ ] Task: Verify that all internal links remain functional.
- [ ] Task: Conductor - User Manual Verification 'Context Cleanup' (Protocol in workflow.md)
- [ ] Task: Execute `py_get_skeleton` and `py_get_code_outline` for `events.py`, `api_hooks.py`, `api_hook_client.py`, and `gui_2.py` to create a technical map for the guides.
- [ ] Task: Analyze the `live_gui` fixture in `tests/conftest.py` and the simulation loop in `tests/visual_sim_mma_v2.py`.
## Phase 2: Core Documentation Refresh
Update the Architecture and Tools guides to reflect recent architectural changes.
## Phase 2: Core Architecture Deep Dive
Update `docs/guide_architecture.md` with expert-level detail.
- [ ] Task: Document the Dual-Threaded App Lifetime: Main GUI loop vs. Daemon execution threads.
- [ ] Task: Detail the `AsyncEventQueue` and `EventEmitter` roles in the decoupling strategy.
- [ ] Task: Explain the `_pending_gui_tasks` synchronization mechanism for bridging the Hook Server and GUI.
- [ ] Task: Document the "Linear Execution Clutch" and its deterministic state machine.
- [ ] Task: Verify the architectural descriptions against the actual implementation.
- [ ] Task: Conductor - User Manual Verification 'Phase 2: Core Architecture Deep Dive' (Protocol in workflow.md)
- [ ] Task: Audit `docs/guide_architecture.md` against current code (e.g., `EventEmitter`, `ApiHookClient`, Conductor).
- [ ] Task: Update `docs/guide_architecture.md` with current Conductor-driven architecture and dual-GUI structure.
- [ ] Task: Audit `docs/guide_tools.md` for toolset accuracy.
- [ ] Task: Update `docs/guide_tools.md` to include API hook client and performance monitoring documentation.
- [ ] Task: Verify documentation alignment with actual implementation.
- [ ] Task: Conductor - User Manual Verification 'Core Documentation Refresh' (Protocol in workflow.md)
## Phase 3: Hook System & Tooling Technical Reference
Update `docs/guide_tools.md` to include low-level API details.
- [ ] Task: Create a comprehensive API reference for all `HookServer` endpoints.
- [ ] Task: Document the `ApiHookClient` implementation, including retries and polling strategies.
- [ ] Task: Update the MCP toolset guide with current native tool implementations.
- [ ] Task: Document the `ask/respond` IPC flow for "Human-in-the-Loop" confirmations.
- [ ] Task: Conductor - User Manual Verification 'Phase 3: Hook System & Tooling Technical Reference' (Protocol in workflow.md)
## Phase 3: README Refresh and Link Validation
Modernize the primary project entry point and ensure documentation integrity.
## Phase 4: Verification & Simulation Framework
Create the new `docs/guide_simulations.md` guide.
- [ ] Task: Detail the Live GUI testing infrastructure: `--enable-test-hooks` and the `live_gui` fixture.
- [ ] Task: Breakdown the Simulation Lifecycle: Startup, Polling, Interaction, and Assertion.
- [ ] Task: Document the mock provider strategy using `tests/mock_gemini_cli.py`.
- [ ] Task: Provide examples of visual verification tests (e.g., MMA lifecycle).
- [ ] Task: Conductor - User Manual Verification 'Phase 4: Verification & Simulation Framework' (Protocol in workflow.md)
- [ ] Task: Audit `Readme.md` for accuracy of setup instructions and feature highlights.
- [ ] Task: Write failing test (or link audit) that identifies outdated setup steps or broken links.
- [ ] Task: Update `Readme.md` with `uv` setup, current project vision, and feature lists (Conductor, GUI 2.0).
- [ ] Task: Perform a project-wide link validation of all Markdown files in `./docs/` and the root.
- [ ] Task: Verify setup instructions by performing a manual walkthrough of the Readme steps.
- [ ] Task: Conductor - User Manual Verification 'README Refresh and Link Validation' (Protocol in workflow.md)
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## Phase 5: README & Roadmap Update
- [ ] Task: Update `Readme.md` with current setup (`uv`, `credentials.toml`) and vision.
- [ ] Task: Perform a project-wide link validation of all Markdown files.
- [ ] Task: Verify the high-density information style across all documentation.
- [ ] Task: Conductor - User Manual Verification 'Phase 5: README & Roadmap Update' (Protocol in workflow.md)