# Implementation Plan: Code Path & Data Pipeline Analysis (code_path_analysis_20260507)

## Phase 1: Structural Exploration & Tooling Setup
- [x] Task: Initialize `PIPELINE_ANALYSIS.md` template.
- [x] Task: Deploy `codebase_investigator` subagents to identify top-level entry points in `gui_2.py` and `simulation/`.
- [x] Task: Verify usage of existing tree-sitter tools to generate initial call-graph skeletons for `./src`.
- [x] Task: Conductor - User Manual Verification 'Phase 1' (Protocol in workflow.md)

## Phase 2: Mapping Core Source Pipelines (`./src`)
- [x] Task: Map the **Context Aggregation Pipeline** (`aggregate.py`, `models.py`).
- [x] Task: Map the **AI Interaction Loop** (`ai_client.py`, `mcp_client.py`, `shell_runner.py`).
- [x] Task: Map the **GUI Event & State Pipeline** (`gui_2.py`, `app_controller.py`).
- [x] Task: Document data responsibilities and state boundaries for each route.
- [x] Task: Conductor - User Manual Verification 'Phase 2' (Protocol in workflow.md)

## Phase 3: Mapping Simulation Pipelines (`./simulation`)
- [x] Task: Map the **Simulation Lifecycle** (`sim_base.py`, `sim_context.py`, `workflow_sim.py`).
- [x] Task: Analyze data flow between `sim_ai_settings.py` and the execution engine.
- [x] Task: Document the "Verification & Checkpointing" route in simulations.
- [x] Task: Conductor - User Manual Verification 'Phase 3' (Protocol in workflow.md)

## Phase 4: Synthesis & Reporting
- [x] Task: Consolidate all findings into Mermaid diagrams within `PIPELINE_ANALYSIS.md`.
- [x] Task: Identify specific "Curation Targets" (redundancies, style violations) for the next track.
- [x] Task: Final review and hand-off to Track 2 (Codebase Curation).
- [x] Task: Conductor - User Manual Verification 'Phase 4' (Protocol in workflow.md)
