chore(conductor): Add index.md to new tracks, archive completed/superseded tracks

- Add index.md to mma_pipeline_fix, simulation_hardening, context_token_viz
- Archive documentation_refresh_20260224 (superseded by 08e003a rewrite)
- Archive robust_live_simulation_verification (context distilled into
  simulation_hardening_20260301 spec)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

conductor/tracks/_archived/documentation_refresh_20260224/index.md

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+# Track documentation_refresh_20260224 Context
+
+- [Specification](./spec.md)
+- [Implementation Plan](./plan.md)
+- [Metadata](./metadata.json)

conductor/tracks/_archived/documentation_refresh_20260224/metadata.json

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+{
+  "track_id": "documentation_refresh_20260224",
+  "type": "chore",
+  "status": "new",
+  "created_at": "2026-02-24T18:35:00Z",
+  "updated_at": "2026-02-24T18:35:00Z",
+  "description": "Update ./docs/* & ./Readme.md, review ./MainContext.md significance (should we keep it..)."
+}

conductor/tracks/_archived/documentation_refresh_20260224/plan.md

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+# Implementation Plan: Deep Architectural Documentation Refresh
+
+## Phase 1: Context Cleanup & Research
+- [x] Task: Audit references to `MainContext.md` across the project.
+- [x] Task: Delete `MainContext.md` and update any identified references.
+- [x] 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.
+- [x] Task: Analyze the `live_gui` fixture in `tests/conftest.py` and the simulation loop in `tests/visual_sim_mma_v2.py`.
+
+## Phase 2: Core Architecture Deep Dive
+Update `docs/guide_architecture.md` with expert-level detail.
+- [x] Task: Document the Dual-Threaded App Lifetime: Main GUI loop vs. Daemon execution threads.
+- [x] Task: Detail the `AsyncEventQueue` and `EventEmitter` roles in the decoupling strategy.
+- [x] Task: Explain the `_pending_gui_tasks` synchronization mechanism for bridging the Hook Server and GUI.
+- [x] Task: Document the "Linear Execution Clutch" and its deterministic state machine.
+- [x] Task: Verify the architectural descriptions against the actual implementation.
+- [x] Task: Conductor - User Manual Verification 'Phase 2: Core Architecture Deep Dive' (Protocol in workflow.md)
+
+## Phase 3: Hook System & Tooling Technical Reference
+Update `docs/guide_tools.md` to include low-level API details.
+- [x] Task: Create a comprehensive API reference for all `HookServer` endpoints.
+- [x] Task: Document the `ApiHookClient` implementation, including retries and polling strategies.
+- [x] Task: Update the MCP toolset guide with current native tool implementations.
+- [x] Task: Document the `ask/respond` IPC flow for "Human-in-the-Loop" confirmations.
+- [x] Task: Conductor - User Manual Verification 'Phase 3: Hook System & Tooling Technical Reference' (Protocol in workflow.md)
+
+## Phase 4: Verification & Simulation Framework
+Create the new `docs/guide_simulations.md` guide.
+- [x] Task: Detail the Live GUI testing infrastructure: `--enable-test-hooks` and the `live_gui` fixture.
+- [x] Task: Breakdown the Simulation Lifecycle: Startup, Polling, Interaction, and Assertion.
+- [x] Task: Document the mock provider strategy using `tests/mock_gemini_cli.py`.
+- [x] Task: Provide examples of visual verification tests (e.g., MMA lifecycle).
+- [x] Task: Conductor - User Manual Verification 'Phase 4: Verification & Simulation Framework' (Protocol in workflow.md)
+
+## Phase 5: README & Roadmap Update
+- [x] Task: Update `Readme.md` with current setup (`uv`, `credentials.toml`) and vision.
+- [x] Task: Perform a project-wide link validation of all Markdown files.
+- [x] Task: Verify the high-density information style across all documentation.
+- [x] Task: Conductor - User Manual Verification 'Phase 5: README & Roadmap Update' (Protocol in workflow.md)

conductor/tracks/_archived/documentation_refresh_20260224/spec.md

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+# Track Specification: Deep Architectural Documentation Refresh
+
+## Overview
+This track implements a high-density, expert-level documentation suite for the Manual Slop project. The documentation style is strictly modeled after the **pedagogical and narrative standards** of `gencpp` and `VEFontCache-Odin`. It moves beyond simple "User Guides" to provide a **"USA Graphics Company"** architectural reference: high information density, tactical technical transparency, and a narrative intent that guides a developer from high-level philosophy to low-level implementation.
+
+## Pedagogical Goals
+1.  **Narrative Intent:** Documentation must transition the reader through a logical learning journey: **Philosophy/Mental Model -> Architectural Boundaries -> Implementation Logic -> Verification/Simulation.**
+2.  **High Information Density:** Eliminate conversational filler and "fluff." Every sentence must provide architectural signal (state transitions, data flows, constraints).
+3.  **Technical Transparency:** Document the "How" and "Why" behind design decisions (e.g., *Why* the dual-threaded `Asyncio` loop? *How* does the "Execution Clutch" bridge the thread gap?).
+4.  **Architectural Mapping:** Use precise symbol names (`AsyncEventQueue`, `_pending_gui_tasks`, `HookServer`) to map the documentation directly to the source code.
+5.  **Multi-Layered Depth:** Each major component (Architecture, Tools, Simulations) must have its own dedicated, expert-level guide. No consolidation into single, shallow files.
+
+## Functional Requirements (Documentation Areas)
+
+### 1. Core Architecture (`docs/guide_architecture.md`)
+-   **System Philosophy:** The "Decoupled State Machine" mental model.
+-   **Application Lifetime:** The multi-threaded boot sequence and the "Dual-Flush" persistence model.
+-   **The Task Pipeline:** Detailed producer-consumer synchronization between the GUI (Main) and AI (Daemon) threads.
+-   **The Execution Clutch (HITL):** Detailed state machine for human-in-the-loop interception and payload mutation.
+
+### 2. Tooling & IPC Reference (`docs/guide_tools.md`)
+-   **MCP Bridge:** Low-level security constraints and filesystem sandboxing.
+-   **Hook API:** A full technical reference for the REST/IPC interface (endpoints, payloads, diagnostics).
+-   **IPC Flow:** The `ask/respond` sequence for synchronous human-in-the-loop requests.
+
+### 3. Verification & Simulation Framework (`docs/guide_simulations.md`)
+-   **Infrastructure:** The `--enable-test-hooks` flag and the `live_gui` pytest fixture.
+-   **Lifecycle:** The "Puppeteer" pattern for driving the GUI via automated clients.
+-   **Mocking Strategy:** Script-based AI provider mocking via `mock_gemini_cli.py`.
+-   **Visual Assertion:** Examples of verifying the rendered state (DAG, Terminal streams) rather than just API returns.
+
+### 4. Product Vision & Roadmap (`Readme.md`)
+-   **Technological Identity:** High-density experimental tool for local AI orchestration.
+-   **Pedagogical Landing:** Direct links to the deep-dive guides to establish the project's expert-level tone immediately.
+
+## Acceptance Criteria for Expert Review (Claude Opus)
+-   [ ] **Zero Filler:** No introductory "In this section..." or "Now we will..." conversational markers.
+-   [ ] **Structural Parity:** Documentation follows the `gencpp` pattern (Philosophy -> Code Paths -> Interface).
+-   [ ] **Expert-Level Detail:** Includes data structures, locking mechanisms, and thread-safety constraints.
+-   [ ] **Narrative Cohesion:** The documents feel like a single, expert-authored manual for a complex graphics or systems engine.
+-   [ ] **Tactile Interaction:** Explains the "Linear Execution Clutch" as a physical shift in the application's processing gears.
+
+## Out of Scope
+-   Documenting legacy `gui_legacy.py` code beyond its role as a fallback.
+-   Visual diagram generation (focusing on high-signal text-based architectural mapping).