chore(conductor): Complete Code Path & Data Pipeline Analysis

conductor/tracks.md

@@ -10,7 +10,7 @@ This file tracks all major tracks for the project. Each track has its own detail
 
 ### Analysis & Structural Review
 
-1. [ ] **Track: Code Path & Data Pipeline Analysis**
+1. [x] **Track: Code Path & Data Pipeline Analysis**
    *Link: [./tracks/code_path_analysis_20260507/](./tracks/code_path_analysis_20260507/)*
    *Goal: Comprehensive analysis of major processing routes in `./src` and `./simulation`. Identify data pipelines and responsibilities. Map core execution flows to inform curation efforts.*
 

conductor/tracks/code_path_analysis_20260507/plan.md

@@ -1,26 +1,26 @@
 # Implementation Plan: Code Path & Data Pipeline Analysis (code_path_analysis_20260507)
 
 ## Phase 1: Structural Exploration & Tooling Setup
-- [ ] Task: Initialize `PIPELINE_ANALYSIS.md` template.
-- [ ] Task: Deploy `codebase_investigator` subagents to identify top-level entry points in `gui_2.py` and `simulation/`.
-- [ ] Task: Verify usage of existing tree-sitter tools to generate initial call-graph skeletons for `./src`.
-- [ ] Task: Conductor - User Manual Verification 'Phase 1' (Protocol in workflow.md)
+- [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`)
-- [ ] Task: Map the **Context Aggregation Pipeline** (`aggregate.py`, `models.py`).
-- [ ] Task: Map the **AI Interaction Loop** (`ai_client.py`, `mcp_client.py`, `shell_runner.py`).
-- [ ] Task: Map the **GUI Event & State Pipeline** (`gui_2.py`, `app_controller.py`).
-- [ ] Task: Document data responsibilities and state boundaries for each route.
-- [ ] Task: Conductor - User Manual Verification 'Phase 2' (Protocol in workflow.md)
+- [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`)
-- [ ] Task: Map the **Simulation Lifecycle** (`sim_base.py`, `sim_context.py`, `workflow_sim.py`).
-- [ ] Task: Analyze data flow between `sim_ai_settings.py` and the execution engine.
-- [ ] Task: Document the "Verification & Checkpointing" route in simulations.
-- [ ] Task: Conductor - User Manual Verification 'Phase 3' (Protocol in workflow.md)
+- [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
-- [ ] Task: Consolidate all findings into Mermaid diagrams within `PIPELINE_ANALYSIS.md`.
-- [ ] Task: Identify specific "Curation Targets" (redundancies, style violations) for the next track.
-- [ ] Task: Final review and hand-off to Track 2 (Codebase Curation).
-- [ ] Task: Conductor - User Manual Verification 'Phase 4' (Protocol in workflow.md)
+- [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)