chore(conductor): Archive completed and deprecated tracks

- Moved codebase_migration_20260302 to archive

- Moved gui_decoupling_controller_20260302 to archive

- Moved test_architecture_integrity_audit_20260304 to archive

- Removed deprecated test_suite_performance_and_flakiness_20260302

conductor/archive/codebase_migration_20260302/index.md

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+# Track codebase_migration_20260302 Context
+
+- [Specification](./spec.md)
+- [Implementation Plan](./plan.md)
+- [Metadata](./metadata.json)

conductor/archive/codebase_migration_20260302/metadata.json

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+{
+  "track_id": "codebase_migration_20260302",
+  "type": "chore",
+  "status": "new",
+  "created_at": "2026-03-02T22:28:00Z",
+  "updated_at": "2026-03-02T22:28:00Z",
+  "description": "Move the codebase from the main directory to a src directory. Alleviate clutter by doing so. Remove files that are not used at all by the current application's implementation."
+}

conductor/archive/codebase_migration_20260302/plan.md

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+# Implementation Plan: Codebase Migration to `src` & Cleanup (codebase_migration_20260302)
+
+## Status: COMPLETE [checkpoint: 92da972]
+
+## Phase 1: Unused File Identification & Removal
+- [x] Task: Initialize MMA Environment `activate_skill mma-orchestrator`
+- [x] Task: Audit Codebase for Dead Files (1eb9d29)
+- [x] Task: Delete Unused Files (1eb9d29)
+- [-] Task: Conductor - User Manual Verification 'Phase 1: Unused File Identification & Removal' (SKIPPED)
+
+## Phase 2: Directory Restructuring & Migration
+- [x] Task: Create `src/` Directory
+- [x] Task: Move Application Files to `src/`
+- [x] Task: Conductor - User Manual Verification 'Phase 2: Directory Restructuring & Migration' (Checkpoint: 24f385e)
+
+## Phase 3: Entry Point & Import Resolution
+- [x] Task: Create `sloppy.py` Entry Point (c102392)
+- [x] Task: Resolve Absolute and Relative Imports (c102392)
+- [x] Task: Conductor - User Manual Verification 'Phase 3: Entry Point & Import Resolution' (Checkpoint: 24f385e)
+## Phase 4: Final Validation & Documentation
+- [x] Task: Full Test Suite Validation (ea5bb4e)
+- [x] Task: Update Core Documentation (ea5bb4e)
+- [x] Task: Conductor - User Manual Verification 'Phase 4: Final Validation & Documentation' (92da972)

conductor/archive/codebase_migration_20260302/spec.md

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+# Track Specification: Codebase Migration to `src` & Cleanup (codebase_migration_20260302)
+
+## Overview
+This track focuses on restructuring the codebase to alleviate clutter by moving the main implementation files from the project root into a dedicated `src/` directory. Additionally, files that are completely unused by the current implementation will be automatically identified and removed. A new clean entry point (`sloppy.py`) will be created in the root directory.
+
+## Functional Requirements
+- **Directory Restructuring**:
+  - Move all active Python implementation files (e.g., `gui_2.py`, `ai_client.py`, `mcp_client.py`, `shell_runner.py`, `project_manager.py`, `events.py`, etc.) into a new `src/` directory.
+  - Update internal imports within all moved files to reflect their new locations or ensure the Python path resolves them correctly.
+- **Root Directory Retention**:
+  - Keep configuration files (e.g., `config.toml`, `pyproject.toml`, `requirements.txt`, `.gitignore`) in the project root.
+  - Keep documentation files and directories (e.g., `Readme.md`, `BUILD.md`, `docs/`) in the project root.
+  - Keep the `tests/` and `simulation/` directories at the root level.
+- **New Entry Point**:
+  - Create a new file `sloppy.py` in the root directory.
+  - `sloppy.py` will serve as the primary entry point to launch the application (jumpstarting the underlying `gui_2.py` logic which will be moved into `src/`).
+- **Dead Code/File Removal**:
+  - Automatically identify completely unused files and scripts in the project root (e.g., legacy files, unreferenced tools).
+  - Delete the identified unused files to clean up the repository.
+
+## Non-Functional Requirements
+- Ensure all automated tests (`tests/`) and simulations (`simulation/`) continue to function perfectly without `ModuleNotFoundError`s.
+- `sloppy.py` must support existing CLI arguments (e.g., `--enable-test-hooks`).
+
+## Acceptance Criteria
+- [ ] A `src/` directory exists and contains the main application logic.
+- [ ] The root directory is clean, containing mainly configs, docs, `tests/`, `simulation/`, and `sloppy.py`.
+- [ ] `sloppy.py` successfully launches the application.
+- [ ] The full test suite runs and passes (i.e. all imports are correctly resolved).
+- [ ] Obsolete/unused files have been successfully deleted from the repository.
+
+## Out of Scope
+- Complete refactoring of `gui_2.py` into a fully modular system (this track only moves it, though preparing it for future non-monolithic structure is conceptually aligned).