chore(conductor): Enhance all 6 backlog tracks to Surgical Spec Protocol

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# Track Specification: GUI Decoupling & Controller Architecture
# Track Specification: GUI Decoupling & Controller Architecture (gui_decoupling_controller_20260302)
## Overview
`gui_2.py` is a monolithic God Object. This track extracts its business logic and state machine into `app_controller.py`, leaving the GUI as a pure immediate-mode view adhering to Data-Oriented Design.
`gui_2.py` currently operates as a Monolithic God Object (3,500+ lines). It violates the Data-Oriented Design heuristic by owning complex business logic, orchestrator hooks, and markdown file building. This track extracts the core state machine and lifecycle into a headless `app_controller.py`, turning the GUI into a pure immediate-mode view.
## Architectural Constraints: The "Immediate Mode View" Contract
- **No Business Logic in View**: `gui_2.py` MUST NOT perform file I/O, AI API calls, or subprocess management directly.
- **State Ownership**: `app_controller.py` (or equivalent) owns the "Source of Truth" state.
- **Event-Driven Mutations**: The GUI must mutate state exclusively by dispatching events or calling controller methods, never by directly manipulating backend objects in the render loop.
## Functional Requirements
- Create `app_controller.py`.
- Migrate state variables and lifecycle methods from `gui_2.py` to the controller.
- Ensure `gui_2.py` only reads state and dispatches events.
- **Controller Extraction**: Create `app_controller.py` to handle all non-rendering logic.
- **State Migration**: Move state variables (`_tool_log`, `_comms_log`, `active_tickets`, etc.) out of `App.__init__` into the controller.
- **Logic Migration**: Move background threads, file reading/writing (`_flush_to_project`), and AI orchestrator invocations to the controller.
- **View Refactoring**: Refactor `gui_2.py` to accept the controller as a dependency and merely render its current state.
## Acceptance Criteria
- [ ] `app_controller.py` exists and owns the application state.
- [ ] `gui_2.py` has been reduced in size and complexity (no file I/O or AI calls).
- [ ] All existing features (chat, tools, tracks) function identically.
- [ ] The full test suite runs and passes against the new decoupled architecture.