fix(gui): Use correct ImVec4 color API in placeholder methods

imgui.ImColor.IM_COL32 doesn't exist - use C_LBL (vec4) instead.
Fixes Missing EndTabBar() error caused by exception in placeholder methods.

.opencode/agents/explore.md

@@ -1,7 +1,7 @@
----
+---
 description: Fast, read-only agent for exploring the codebase structure
 mode: subagent
-model: MiniMax-M2.5
+model: minimax-coding-plan/MiniMax-M2.7
 temperature: 0.2
 permission:
   edit: deny
@@ -78,4 +78,4 @@ Return concise findings with file:line references:
 
 ### Summary
 [One-paragraph summary of findings]
-```
+```

.opencode/agents/general.md

@@ -1,7 +1,7 @@
----
+---
 description: General-purpose agent for researching complex questions and executing multi-step tasks
 mode: subagent
-model: MiniMax-M2.5
+model: minimax-coding-plan/MiniMax-M2.7
 temperature: 0.3
 ---
 
@@ -81,4 +81,4 @@ Return detailed findings with evidence:
 
 ### Recommendations
 - [Suggested next steps if applicable]
-```
+```

.opencode/agents/tier1-orchestrator.md

@@ -1,7 +1,7 @@
----
+---
 description: Tier 1 Orchestrator for product alignment, high-level planning, and track initialization
 mode: primary
-model: MiniMax-M2.5
+model: minimax-coding-plan/MiniMax-M2.7
 temperature: 0.5
 permission:
   edit: ask
@@ -18,7 +18,7 @@ ONLY output the requested text. No pleasantries.
 
 ## Context Management
 
-**MANUAL COMPACTION ONLY** — Never rely on automatic context summarization.
+**MANUAL COMPACTION ONLY** <EFBFBD> Never rely on automatic context summarization.
 Use `/compact` command explicitly when context needs reduction.
 Preserve full context during track planning and spec creation.
 
@@ -105,7 +105,7 @@ Use `manual-slop_py_get_code_outline`, `manual-slop_py_get_definition`,
 Document existing implementations with file:line references in a
 "Current State Audit" section in the spec.
 
-**FAILURE TO AUDIT = TRACK FAILURE** — Previous tracks failed because specs
+**FAILURE TO AUDIT = TRACK FAILURE** <EFBFBD> Previous tracks failed because specs
 asked to implement features that already existed.
 
 ### 2. Identify Gaps, Not Features
@@ -175,4 +175,4 @@ Focus: {One-sentence scope}
 - Do NOT use native `edit` tool - use MCP tools
 - DO NOT SKIP A TEST IN PYTEST JUST BECAUSE ITS BROKEN AND HAS NO TRIVIAL SOLUTION OR FIX.
 - DO NOT SIMPLIFY A TEST JUST BECAUSE IT HAS NO TRIVIAL SOLUTION TO FIX.
-- DO NOT CREATE MOCK PATCHES TO PSEUDO API CALLS OR HOOKS BECAUSE THE APP SOURCE WAS CHANGED. ADAPT TESTS PROPERLY.
+- DO NOT CREATE MOCK PATCHES TO PSEUDO API CALLS OR HOOKS BECAUSE THE APP SOURCE WAS CHANGED. ADAPT TESTS PROPERLY.

.opencode/agents/tier2-tech-lead.md

@@ -1,7 +1,7 @@
----
+---
 description: Tier 2 Tech Lead for architectural design and track execution with persistent memory
 mode: primary
-model: MiniMax-M2.5
+model: minimax-coding-plan/MiniMax-M2.7
 temperature: 0.4
 permission:
   edit: ask
@@ -14,9 +14,9 @@ ONLY output the requested text. No pleasantries.
 
 ## Context Management
 
-**MANUAL COMPACTION ONLY** — Never rely on automatic context summarization.
+**MANUAL COMPACTION ONLY** <EFBFBD> Never rely on automatic context summarization.
 Use `/compact` command explicitly when context needs reduction.
-You maintain PERSISTENT MEMORY throughout track execution — do NOT apply Context Amnesia to your own session.
+You maintain PERSISTENT MEMORY throughout track execution <EFBFBD> do NOT apply Context Amnesia to your own session.
 
 ## CRITICAL: MCP Tools Only (Native Tools Banned)
 
@@ -134,14 +134,14 @@ Before implementing:
 - Zero-assertion ban: Tests MUST have meaningful assertions
 - Delegate test creation to Tier 3 Worker via Task tool
 - Run tests and confirm they FAIL as expected
-- **CONFIRM FAILURE** — this is the Red phase
+- **CONFIRM FAILURE** <EFBFBD> this is the Red phase
 
 ### 3. Green Phase: Implement to Pass
 
 - **Pre-delegation checkpoint**: Stage current progress (`git add .`)
 - Delegate implementation to Tier 3 Worker via Task tool
 - Run tests and confirm they PASS
-- **CONFIRM PASS** — this is the Green phase
+- **CONFIRM PASS** <EFBFBD> this is the Green phase
 
 ### 4. Refactor Phase (Optional)
 
@@ -213,4 +213,4 @@ When all tasks in a phase are complete:
 - Do NOT use native `edit` tool - use MCP tools
 - DO NOT SKIP A TEST IN PYTEST JUST BECAUSE ITS BROKEN AND HAS NO TRIVIAL SOLUTION OR FIX.
 - DO NOT SIMPLIFY A TEST JUST BECAUSE IT HAS NO TRIVIAL SOLUTION TO FIX.
-- DO NOT CREATE MOCK PATCHES TO PSEUDO API CALLS OR HOOKS BECAUSE THE APP SOURCE WAS CHANGED. ADAPT TESTS PROPERLY.
+- DO NOT CREATE MOCK PATCHES TO PSEUDO API CALLS OR HOOKS BECAUSE THE APP SOURCE WAS CHANGED. ADAPT TESTS PROPERLY.

.opencode/agents/tier3-worker.md

@@ -1,7 +1,7 @@
----
+---
 description: Stateless Tier 3 Worker for surgical code implementation and TDD
 mode: subagent
-model: MiniMax-M2.5
+model: minimax-coding-plan/minimax-m2.7
 temperature: 0.3
 permission:
   edit: allow
@@ -133,4 +133,4 @@ If you cannot complete the task:
 - Do NOT modify files outside the specified scope
 - DO NOT SKIP A TEST IN PYTEST JUST BECAUSE ITS BROKEN AND HAS NO TRIVIAL SOLUTION OR FIX.
 - DO NOT SIMPLIFY A TEST JUST BECAUSE IT HAS NO TRIVIAL SOLUTION TO FIX.
-- DO NOT CREATE MOCK PATCHES TO PSEUDO API CALLS OR HOOKS BECAUSE THE APP SOURCE WAS CHANGED. ADAPT TESTS PROPERLY.
+- DO NOT CREATE MOCK PATCHES TO PSEUDO API CALLS OR HOOKS BECAUSE THE APP SOURCE WAS CHANGED. ADAPT TESTS PROPERLY.

.opencode/agents/tier4-qa.md

@@ -1,7 +1,7 @@
----
+---
 description: Stateless Tier 4 QA Agent for error analysis and diagnostics
 mode: subagent
-model: MiniMax-M2.5
+model: 	minimax-coding-plan/MiniMax-M2.7
 temperature: 0.2
 permission:
   edit: deny
@@ -119,4 +119,4 @@ If you cannot analyze the error:
 - Do NOT read full large files - use skeleton tools first
 - DO NOT SKIP A TEST IN PYTEST JUST BECAUSE ITS BROKEN AND HAS NO TRIVIAL SOLUTION OR FIX.
 - DO NOT SIMPLIFY A TEST JUST BECAUSE IT HAS NO TRIVIAL SOLUTION TO FIX.
-- DO NOT CREATE MOCK PATCHES TO PSEUDO API CALLS OR HOOKS BECAUSE THE APP SOURCE WAS CHANGED. ADAPT TESTS PROPERLY.
+- DO NOT CREATE MOCK PATCHES TO PSEUDO API CALLS OR HOOKS BECAUSE THE APP SOURCE WAS CHANGED. ADAPT TESTS PROPERLY.

conductor/product.md

@@ -17,7 +17,7 @@ For deep implementation details when planning or implementing tracks, consult `d
 ## Primary Use Cases
 
 - **Full Control over Vendor APIs:** Exposing detailed API metrics and configuring deep agent capabilities directly within the GUI.
-- **Context & Memory Management:** Better visualization and management of token usage and context memory. Includes granular per-file flags (**Auto-Aggregate**, **Force Full**) and a dedicated **'Context' role** for manual injections, allowing developers to optimize prompt limits with expert precision.
+- **Context & Memory Management:** Better visualization and management of token usage and context memory. Includes granular per-file flags (**Auto-Aggregate**, **Force Full**), a dedicated **'Context' role** for manual injections, and **Context Presets** for saving and loading named file/screenshot selections. Allows assigning specific context presets to MMA agent personas for granular cognitive load isolation.
 - **Manual "Vibe Coding" Assistant:** Serving as an auxiliary, multi-provider assistant that natively interacts with the codebase via sandboxed PowerShell scripts and MCP-like file tools, emphasizing manual developer oversight and explicit confirmation.
 
 ## Key Features
@@ -33,6 +33,7 @@ For deep implementation details when planning or implementing tracks, consult `d
     - **Track Browser:** Real-time visualization of all implementation tracks with status indicators and progress bars. Includes a dedicated **Active Track Summary** featuring a color-coded progress bar, precise ticket status breakdown (Completed, In Progress, Blocked, Todo), and dynamic **ETA estimation** based on historical completion times.
     - **Visual Task DAG:** An interactive, node-based visualizer for the active track's task dependencies using `imgui-node-editor`. Features color-coded state tracking (Ready, Running, Blocked, Done), drag-and-drop dependency creation, and right-click deletion.
     - **Strategy Visualization:** Dedicated real-time output streams for Tier 1 (Strategic Planning) and Tier 2/3 (Execution) agents, allowing the user to follow the agent's reasoning chains alongside the task DAG.
+    - **Agent-Focused Filtering:** Allows the user to focus the entire GUI (Session Hub, Discussion Hub, Comms) on a specific agent's activities and scoped context.
   - **Track-Scoped State Management:** Segregates discussion history and task progress into per-track state files. Supports **Project-Specific Conductor Directories**, defaulting to `./conductor` relative to each project's TOML file. Projects can define their own conductor path override in `manual_slop.toml` (`[conductor].dir`) via the Projects tab for isolated track management. This prevents global context pollution and ensures the Tech Lead session is isolated to the specific track's objective.
   **Native DAG Execution Engine:** Employs a Python-based Directed Acyclic Graph (DAG) engine to manage complex task dependencies. Supports automated topological sorting, robust cycle detection, and **transitive blocking propagation** (cascading `blocked` status to downstream dependents to prevent execution stalls).
 
@@ -54,7 +55,9 @@ For deep implementation details when planning or implementing tracks, consult `d
 - **High-Fidelity Selectable UI:** Most read-only labels and logs across the interface (including discussion history, comms payloads, tool outputs, and telemetry metrics) are now implemented as selectable text fields. This enables standard OS-level text selection and copying (Ctrl+C) while maintaining a high-density, non-editable aesthetic.
 - **High-Fidelity UI Rendering:** Employs advanced 3x font oversampling and sub-pixel positioning to ensure crisp, high-clarity text rendering across all resolutions, enhancing readability for dense logs and complex code fragments.
 - **Enhanced MMA Observability:** Worker streams and ticket previews now support direct text selection, allowing for easy extraction of specific logs or reasoning fragments during parallel execution.
-- **Detailed History Management:** Rich discussion history with branching, timestamping, and specific git commit linkage per conversation.
+- **Transparent Context Visibility:** A dedicated **Session Hub** exposes the exact aggregated markdown and resolved system prompt sent to the AI.
+- **Injection Timeline:** Discussion history visually indicates the precise moments when files or screenshots were injected into the session context.
+- **Detailed History Management:** Rich discussion history with non-linear timeline branching ("takes"), tabbed interface navigation, specific git commit linkage per conversation, and automated multi-take synthesis.
 - **Advanced Log Management:** Optimizes log storage by offloading large data (AI-generated scripts and tool outputs) to unique files within the session directory, using compact `[REF:filename]` pointers in JSON-L logs to minimize token overhead during analysis. Features a dedicated **Log Management panel** for monitoring, whitelisting, and pruning session logs.
 - **Full Session Restoration:** Allows users to load and reconstruct entire historical sessions from their log directories. Includes a dedicated, tinted **'Historical Replay' mode** that populates discussion history and provides a read-only view of prior agent activities.
 - **Dedicated Diagnostics Hub:** Consolidates real-time telemetry (FPS, CPU, Frame Time) and transient system warnings into a standalone **Diagnostics panel**, providing deep visibility into application health without polluting the discussion history.

conductor/tracks.md

@@ -1,4 +1,4 @@
-# Project Tracks
+# Project Tracks
 
 This file tracks all major tracks for the project. Each track has its own detailed plan in its respective folder.
 
@@ -35,8 +35,16 @@ This file tracks all major tracks for the project. Each track has its own detail
 7. [ ] **Track: Optimization pass for Data-Oriented Python heuristics**
     *Link: [./tracks/data_oriented_optimization_20260312/](./tracks/data_oriented_optimization_20260312/)*
 
-8. [ ] **Track: Rich Thinking Trace Handling**
-    *Link: [./tracks/thinking_trace_handling_20260313/](./tracks/thinking_trace_handling_20260313/)*
+ 8. [x] **Track: Rich Thinking Trace Handling** - *Parse and display AI thinking/reasoning traces*
+   *Link: [./tracks/thinking_trace_handling_20260313/](./tracks/thinking_trace_handling_20260313/)*
+
+ 9. [ ] **Track: Smarter Aggregation with Sub-Agent Summarization**
+    *Link: [./tracks/aggregation_smarter_summaries_20260322/](./tracks/aggregation_smarter_summaries_20260322/)*
+    *Goal: Sub-agent summarization during aggregation pass, hash-based caching for file summaries, smart outline generation for code vs text files.*
+
+ 10. [ ] **Track: System Context Exposure**
+     *Link: [./tracks/system_context_exposure_20260322/](./tracks/system_context_exposure_20260322/)*
+     *Goal: Expose hidden _SYSTEM_PROMPT from ai_client.py to users for customization via AI Settings.*
 
 ---
 
@@ -60,31 +68,32 @@ This file tracks all major tracks for the project. Each track has its own detail
 
 5. [x] **Track: NERV UI Theme Integration** (Archived 2026-03-09)
 
-6. [ ] **Track: Custom Shader and Window Frame Support** 
+6. [X] **Track: Custom Shader and Window Frame Support** 
    *Link: [./tracks/custom_shaders_20260309/](./tracks/custom_shaders_20260309/)*
 
 7. [x] **Track: UI/UX Improvements - Presets and AI Settings**
    *Link: [./tracks/presets_ai_settings_ux_20260311/](./tracks/presets_ai_settings_ux_20260311/)*
    *Goal: Improve the layout, scaling, and control ergonomics of the Preset windows (Personas, Prompts, Tools) and AI Settings panel. Includes dual-control sliders and categorized tool management.*
 
-8. [ ] **Track: Session Context Snapshots & Visibility**
+8. [x] ~~**Track: Session Context Snapshots & Visibility**~~ (Archived 2026-03-22 - Replaced by discussion_hub_panel_reorganization)
    *Link: [./tracks/session_context_snapshots_20260311/](./tracks/session_context_snapshots_20260311/)*
    *Goal: Session-scoped context management, saving Context Presets, MMA assignment, and agent-focused session filtering in the UI.*
 
-9. [ ] **Track: Discussion Takes & Timeline Branching**
+9. [x] ~~**Track: Discussion Takes & Timeline Branching**~~ (Archived 2026-03-22 - Replaced by discussion_hub_panel_reorganization)
    *Link: [./tracks/discussion_takes_branching_20260311/](./tracks/discussion_takes_branching_20260311/)*
    *Goal: Non-linear discussion timelines via tabbed "takes", message branching, and synthesis generation workflows.*
 
+12. [ ] **Track: Discussion Hub Panel Reorganization**
+    *Link: [./tracks/discussion_hub_panel_reorganization_20260322/](./tracks/discussion_hub_panel_reorganization_20260322/)*
+    *Goal: Properly merge Session Hub into Discussion Hub (4 tabs: Discussion | Context Composition | Snapshot | Takes), establish Files & Media as project-level inventory, deprecate ui_summary_only, implement Context Composition and DAW-style Takes.*
+
 10. [ ] **Track: Undo/Redo History Support**
     *Link: [./tracks/undo_redo_history_20260311/](./tracks/undo_redo_history_20260311/)*
     *Goal: Robust, non-provider based undo/redo for text inputs, UI controls, discussion mutations, and context management. Includes hotkey support and a history list view.*
 
-11. [ ] **Track: Advanced Text Viewer with Syntax Highlighting**
+11. [x] **Track: Advanced Text Viewer with Syntax Highlighting**
     *Link: [./tracks/text_viewer_rich_rendering_20260313/](./tracks/text_viewer_rich_rendering_20260313/)*
 
-12. [ ] **Track: Frosted Glass Background Effect**
-    *Link: [./tracks/frosted_glass_20260313/](./tracks/frosted_glass_20260313/)*
-
 ---
 
 ### Additional Language Support
@@ -164,6 +173,10 @@ This file tracks all major tracks for the project. Each track has its own detail
 
 ### Completed / Archived
 
+-. [ ] ~~**Track: Frosted Glass Background Effect**~~ ***NOT WORTH THE PAIN***
+    *Link: [./tracks/frosted_glass_20260313/](./tracks/frosted_glass_20260313/)*
+
+
 - [x] **Track: External MCP Server Support** (Archived 2026-03-12)
 - [x] **Track: Project-Specific Conductor Directory** (Archived 2026-03-12)
 - [x] **Track: GUI Path Configuration in Context Hub** (Archived 2026-03-12)

conductor/tracks/aggregation_smarter_summaries_20260322/metadata.json

@@ -0,0 +1,17 @@
+{
+  "name": "aggregation_smarter_summaries",
+  "created": "2026-03-22",
+  "status": "future",
+  "priority": "medium",
+  "affected_files": [
+    "src/aggregate.py",
+    "src/file_cache.py",
+    "src/ai_client.py",
+    "src/models.py"
+  ],
+  "related_tracks": [
+    "discussion_hub_panel_reorganization (in_progress)",
+    "system_context_exposure (future)"
+  ],
+  "notes": "Deferred from discussion_hub_panel_reorganization planning. Improves aggregation with sub-agent summarization and hash-based caching."
+}

conductor/tracks/aggregation_smarter_summaries_20260322/plan.md

@@ -0,0 +1,49 @@
+# Implementation Plan: Smarter Aggregation with Sub-Agent Summarization
+
+## Phase 1: Hash-Based Summary Cache
+Focus: Implement file hashing and cache storage
+
+- [ ] Task: Research existing file hash implementations in codebase
+- [ ] Task: Design cache storage format (file-based vs project state)
+- [ ] Task: Implement hash computation for aggregation files
+- [ ] Task: Implement summary cache storage and retrieval
+- [ ] Task: Add cache invalidation when file content changes
+- [ ] Task: Write tests for hash computation and cache
+- [ ] Task: Conductor - User Manual Verification 'Phase 1: Hash-Based Summary Cache'
+
+## Phase 2: Sub-Agent Summarization
+Focus: Implement sub-agent summarization during aggregation
+
+- [ ] Task: Audit current aggregate.py flow
+- [ ] Task: Define summarization prompt strategy for code vs text files
+- [ ] Task: Implement sub-agent invocation during aggregation
+- [ ] Task: Handle provider-specific differences in sub-agent calls
+- [ ] Task: Write tests for sub-agent summarization
+- [ ] Task: Conductor - User Manual Verification 'Phase 2: Sub-Agent Summarization'
+
+## Phase 3: Tiered Aggregation Strategy
+Focus: Respect tier-level aggregation configuration
+
+- [ ] Task: Audit how tiers receive context currently
+- [ ] Task: Implement tier-level aggregation strategy selection
+- [ ] Task: Connect tier strategy to Persona configuration
+- [ ] Task: Write tests for tiered aggregation
+- [ ] Task: Conductor - User Manual Verification 'Phase 3: Tiered Aggregation Strategy'
+
+## Phase 4: UI Integration
+Focus: Expose cache status and controls in UI
+
+- [ ] Task: Add cache status indicator to Files & Media panel
+- [ ] Task: Add "Clear Summary Cache" button
+- [ ] Task: Add aggregation configuration to Project Settings or AI Settings
+- [ ] Task: Write tests for UI integration
+- [ ] Task: Conductor - User Manual Verification 'Phase 4: UI Integration'
+
+## Phase 5: Cache Persistence & Optimization
+Focus: Ensure cache persists and is performant
+
+- [ ] Task: Implement persistent cache storage to disk
+- [ ] Task: Add cache size management (max entries, LRU)
+- [ ] Task: Performance testing with large codebases
+- [ ] Task: Write tests for persistence
+- [ ] Task: Conductor - User Manual Verification 'Phase 5: Cache Persistence & Optimization'

conductor/tracks/aggregation_smarter_summaries_20260322/spec.md

@@ -0,0 +1,103 @@
+# Specification: Smarter Aggregation with Sub-Agent Summarization
+
+## 1. Overview
+
+This track improves the context aggregation system to use sub-agent passes for intelligent summarization and hash-based caching to avoid redundant work.
+
+**Current Problem:**
+- Aggregation is a simple pass that either injects full file content or a basic skeleton
+- No intelligence applied to determine what level of detail is needed
+- Same files get re-summarized on every discussion start even if unchanged
+
+**Goal:**
+- Use a sub-agent during aggregation pass for high-tier agents to generate succinct summaries
+- Cache summaries based on file hash - only re-summarize if file changed
+- Smart outline generation for code files, summary for text files
+
+## 2. Current State Audit
+
+### Existing Aggregation Behavior
+- `aggregate.py` handles context aggregation
+- `file_cache.py` provides AST parsing and skeleton generation
+- Per-file flags: `Auto-Aggregate` (summarize), `Force Full` (inject raw)
+- No caching of summarization results
+
+### Provider API Considerations
+- Different providers have different prompt/caching mechanisms
+- Need to verify how each provider handles system context and caching
+- May need provider-specific aggregation strategies
+
+## 3. Functional Requirements
+
+### 3.1 Hash-Based Summary Cache
+- Generate SHA256 hash of file content
+- Store summaries in a cache (file-based or in project state)
+- Before summarizing, check if file hash matches cached summary
+- Cache invalidation when file content changes
+
+### 3.2 Sub-Agent Summarization Pass
+- During aggregation, optionally invoke sub-agent for summarization
+- Sub-agent generates concise summary of file purpose and key points
+- Different strategies for:
+  - Code files: AST-based outline + key function signatures
+  - Text files: Paragraph-level summary
+  - Config files: Key-value extraction
+
+### 3.3 Tiered Aggregation Strategy
+- Tier 3/4 workers: Get skeleton outlines (fast, cheap)
+- Tier 2 (Tech Lead): Get summaries with key details
+- Tier 1 (Orchestrator): May get full content or enhanced summaries
+- Configurable per-agent via Persona
+
+### 3.4 Cache Persistence
+- Summaries persist across sessions
+- Stored in project directory or centralized cache location
+- Manual cache clear option in UI
+
+## 4. Data Model
+
+### 4.1 Summary Cache Entry
+```python
+{
+    "file_path": str,
+    "file_hash": str,  # SHA256 of content
+    "summary": str,
+    "outline": str,  # For code files
+    "generated_at": str,  # ISO timestamp
+    "generator_tier": str,  # Which tier generated it
+}
+```
+
+### 4.2 Aggregation Config
+```toml
+[aggregation]
+default_mode = "summarize"  # "full", "summarize", "outline"
+cache_enabled = true
+cache_dir = ".slop_cache"
+```
+
+## 5. UI Changes
+
+- Add "Clear Summary Cache" button in Files & Media or Context Composition
+- Show cached status indicator on files (similar to AST cache indicator)
+- Configuration in AI Settings or Project Settings
+
+## 6. Acceptance Criteria
+
+- [ ] File hash computed before summarization
+- [ ] Summary cache persists across app restarts
+- [ ] Sub-agent generates better summaries than basic skeleton
+- [ ] Aggregation respects tier-level configuration
+- [ ] Cache can be manually cleared
+- [ ] Provider APIs handle aggregated context correctly
+
+## 7. Out of Scope
+- Changes to provider API internals
+- Vector store / embeddings for RAG (separate track)
+- Changes to Session Hub / Discussion Hub layout
+
+## 8. Dependencies
+- `aggregate.py` - main aggregation logic
+- `file_cache.py` - AST parsing and caching
+- `ai_client.py` - sub-agent invocation
+- `models.py` - may need new config structures

conductor/tracks/discussion_hub_panel_reorganization_20260322/metadata.json

@@ -0,0 +1,22 @@
+{
+  "name": "discussion_hub_panel_reorganization",
+  "created": "2026-03-22",
+  "status": "in_progress",
+  "priority": "high",
+  "affected_files": [
+    "src/gui_2.py",
+    "src/models.py",
+    "src/project_manager.py",
+    "tests/test_gui_context_presets.py",
+    "tests/test_discussion_takes.py"
+  ],
+  "replaces": [
+    "session_context_snapshots_20260311",
+    "discussion_takes_branching_20260311"
+  ],
+  "related_tracks": [
+    "aggregation_smarter_summaries (future)",
+    "system_context_exposure (future)"
+  ],
+  "notes": "These earlier tracks were marked complete but the UI panel reorganization was not properly implemented. This track consolidates and properly executes the intended UX."
+}

conductor/tracks/discussion_hub_panel_reorganization_20260322/plan.md

@@ -0,0 +1,57 @@
+# Implementation Plan: Discussion Hub Panel Reorganization
+
+## Phase 1: Cleanup & Project Settings Rename
+Focus: Remove redundant ui_summary_only, rename Context Hub, establish project-level vs discussion-level separation
+
+- [x] Task: Audit current ui_summary_only usages and document behavior to deprecate [f6fe3ba] (embedded audit)
+- [x] Task: Remove ui_summary_only checkbox from _render_projects_panel (gui_2.py) [f5d4913]
+- [x] Task: Rename Context Hub to "Project Settings" in _gui_func tab bar [2ed9867]
+- [ ] Task: Remove Context Presets tab from Project Settings (Context Hub)
+- [ ] Task: Rename Context Hub to "Project Settings" in _gui_func tab bar
+- [x] Task: Remove Context Presets tab from Project Settings (Context Hub) [9ddbcd2]
+- [x] Task: Update references in show_windows dict and any help text [2ed9867] (renamed Context Hub -> Project Settings)
+- [x] Task: Write tests verifying ui_summary_only removal doesn't break existing functionality [f5d4913]
+- [ ] Task: Conductor - User Manual Verification 'Phase 1: Cleanup & Project Settings Rename'
+
+## Phase 2: Merge Session Hub into Discussion Hub [checkpoint: 2b73745]
+Focus: Move Session Hub tabs into Discussion Hub, eliminate separate Session Hub window
+
+- [x] Task: Audit Session Hub (_render_session_hub) tab content [documented above]
+- [x] Task: Add Snapshot tab to Discussion Hub containing Aggregate MD + System Prompt preview [2b73745]
+- [x] Task: Remove Session Hub window from _gui_func [2b73745]
+- [x] Task: Add Discussion Hub tab bar structure (Discussion | Context Composition | Snapshot | Takes) [2b73745]
+- [x] Task: Write tests for new tab structure rendering [2b73745]
+- [x] Task: Conductor - User Manual Verification 'Phase 2: Merge Session Hub into Discussion Hub'
+
+## Phase 3: Context Composition Tab
+Focus: Per-discussion file filter with save/load preset functionality
+
+- [ ] Task: Write tests for Context Composition state management
+- [ ] Task: Create _render_context_composition_panel method
+- [ ] Task: Implement file/screenshot selection display (filtered from Files & Media)
+- [ ] Task: Implement per-file flags display (Auto-Aggregate, Force Full)
+- [ ] Task: Implement Save as Preset / Load Preset buttons
+- [ ] Task: Connect Context Presets storage to this panel
+- [ ] Task: Update Persona editor to reference Context Composition presets
+- [ ] Task: Write tests for Context Composition preset save/load
+- [ ] Task: Conductor - User Manual Verification 'Phase 3: Context Composition Tab'
+
+## Phase 4: Takes Timeline Integration
+Focus: DAW-style branching with proper visual timeline and synthesis
+
+- [ ] Task: Audit existing takes data structure and synthesis_formatter
+- [ ] Task: Enhance takes data model with parent_entry and parent_take tracking
+- [ ] Task: Implement Branch from Entry action in discussion history
+- [ ] Task: Implement visual timeline showing take divergence
+- [ ] Task: Integrate synthesis panel into Takes tab
+- [ ] Task: Implement take selection for synthesis
+- [ ] Task: Write tests for take branching and synthesis
+- [ ] Task: Conductor - User Manual Verification 'Phase 4: Takes Timeline Integration'
+
+## Phase 5: Final Integration & Cleanup
+Focus: Ensure all panels work together, remove dead code
+
+- [ ] Task: Run full test suite to verify no regressions
+- [ ] Task: Remove dead code from ui_summary_only references
+- [ ] Task: Update conductor/tracks.md to mark old session_context_snapshots and discussion_takes_branching as archived/replaced
+- [ ] Task: Conductor - User Manual Verification 'Phase 5: Final Integration & Cleanup'

conductor/tracks/discussion_hub_panel_reorganization_20260322/spec.md

@@ -0,0 +1,137 @@
+# Specification: Discussion Hub Panel Reorganization
+
+## 1. Overview
+
+This track addresses the fragmented implementation of Session Context Snapshots and Discussion Takes & Timeline Branching tracks (2026-03-11). Those tracks were marked complete but the UI panel layout was not properly reorganized.
+
+**Goal:** Create a coherent Discussion Hub that absorbs Session Hub functionality, establishes Files & Media as project-level file inventory, and properly implements Context Composition and DAW-style Takes branching.
+
+## 2. Current State Audit (as of 2026-03-22)
+
+### Already Implemented (DO NOT re-implement)
+- `ui_summary_only` checkbox in Projects panel
+- Session Hub as separate window with tabs: Aggregate MD | System Prompt
+- Context Hub with tabs: Projects | Paths | Context Presets
+- Context Presets save/load mechanism in project TOML
+- `_render_synthesis_panel()` method (gui_2.py:2612-2643) - basic synthesis UI
+- Takes data structure in `project['discussion']['discussions']`
+- Per-file `Auto-Aggregate` and `Force Full` flags in Files & Media
+
+### Gaps to Fill (This Track's Scope)
+1. `ui_summary_only` is redundant with per-file flags - deprecate it
+2. Context Hub renamed to "Project Settings" (remove Context Presets tab)
+3. Session Hub merged into Discussion Hub as tabs
+4. Files & Media stays separate as project-level inventory
+5. Context Composition tab in Discussion Hub for per-discussion filter
+6. Context Presets accessible via Context Composition (save/load filters)
+7. DAW-style Takes timeline properly integrated into Discussion Hub
+8. Synthesis properly integrated with Take selection
+
+## 3. Panel Layout Target
+
+| Panel | Location | Purpose |
+|-------|----------|---------|
+| **AI Settings** | Separate dockable | Provider, model, system prompts, tool presets, bias profiles |
+| **Files & Media** | Separate dockable | Project-level file inventory (addressable files) |
+| **Project Settings** | Context Hub → rename | Git dir, paths, project list (NO context stuff) |
+| **Discussion Hub** | Main hub | All discussion-related UI (tabs below) |
+| **MMA Dashboard** | Separate dockable | Multi-agent orchestration |
+| **Operations Hub** | Separate dockable | Tool calls, comms history, external tools |
+| **Diagnostics** | Separate dockable | Telemetry, logs |
+
+**Discussion Hub Tabs:**
+1. **Discussion** - Main conversation view (current implementation)
+2. **Context Composition** - File/screenshot filter + presets (NEW)
+3. **Snapshot** - Aggregate MD + System Prompt preview (moved from Session Hub)
+4. **Takes** - DAW-style timeline branching + synthesis (integrated, not separate panel)
+
+## 4. Functional Requirements
+
+### 4.1 Deprecate ui_summary_only
+- Remove `ui_summary_only` checkbox from Projects panel
+- Per-file flags (`Auto-Aggregate`, `Force Full`) are the intended mechanism
+- Document migration path for users
+
+### 4.2 Rename Context Hub → Project Settings
+- Context Hub tab bar: Projects | Paths
+- Remove "Context Presets" tab
+- All context-related functionality moves to Discussion Hub → Context Composition
+
+### 4.3 Merge Session Hub into Discussion Hub
+- Session Hub window eliminated
+- Its content becomes tabs in Discussion Hub:
+  - **Snapshot tab**: Aggregate MD preview, System Prompt preview, "Copy" buttons
+  - These were previously in Session Hub
+
+### 4.4 Context Composition Tab (NEW)
+- Shows currently selected files/screenshots for THIS discussion
+- Per-file flags: Auto-Aggregate, Force Full
+- **"Save as Preset"** / **"Load Preset"** buttons
+- Dropdown to select from saved presets
+- Relationship to Files & Media:
+  - Files & Media = the inventory (project-level)
+  - Context Composition = selected filter for current discussion
+
+### 4.5 Takes Timeline (DAW-Style)
+- **New Take**: Start fresh discussion thread
+- **Branch Take**: Fork from any discussion entry
+- **Switch Take**: Make a take the active discussion
+- **Rename/Delete Take**
+- All takes share the same Files & Media (not duplicated)
+- Non-destructive branching
+- Visual timeline showing divergence points
+
+### 4.6 Synthesis Integration
+- User selects 2+ takes via checkboxes
+- Click "Synthesize" button
+- AI generates "resolved" response considering all selected approaches
+- Result appears as new take
+- Accessible from Discussion Hub → Takes tab
+
+## 5. Data Model Changes
+
+### 5.1 Discussion State Structure
+```python
+# Per discussion in project['discussion']['discussions']
+{
+    "name": str,
+    "history": [
+        {"role": "user"|"assistant", "content": str, "ts": str, "files_injected": [...]}
+    ],
+    "parent_entry": Optional[int],  # index of parent message if branched
+    "parent_take": Optional[str],   # name of parent take if branched
+}
+```
+
+### 5.2 Context Preset Format
+```toml
+[context_preset.my_filter]
+files = ["path/to/file_a.py"]
+auto_aggregate = true
+force_full = false
+screenshots = ["path/to/shot1.png"]
+```
+
+## 6. Non-Functional Requirements
+- All changes must not break existing tests
+- New tests required for new functionality
+- Follow 1-space indentation Python code style
+- No comments unless explicitly requested
+
+## 7. Acceptance Criteria
+
+- [ ] `ui_summary_only` removed from Projects panel
+- [ ] Context Hub renamed to Project Settings
+- [ ] Session Hub window eliminated
+- [ ] Discussion Hub has 4 tabs: Discussion, Context Composition, Snapshot, Takes
+- [ ] Context Composition allows save/load of filter presets
+- [ ] Takes can be branched from any entry
+- [ ] Takes timeline shows divergence visually
+- [ ] Synthesis works with 2+ selected takes
+- [ ] All existing tests still pass
+- [ ] New tests cover new functionality
+
+## 8. Out of Scope
+- Aggregation improvements (sub-agent summarization, hash-based caching) - separate future track
+- System prompt exposure (`_SYSTEM_PROMPT` in ai_client.py) - separate future track
+- Session sophistication (Session as container for multiple discussions) - deferred

conductor/tracks/discussion_takes_branching_20260311/plan.md

@@ -1,25 +1,28 @@
 # Implementation Plan: Discussion Takes & Timeline Branching
 
-## Phase 1: Backend Support for Timeline Branching
-- [ ] Task: Write failing tests for extending the session state model to support branching (tree-like history or parallel linear "takes" with a shared ancestor).
-- [ ] Task: Implement backend logic to branch a session history at a specific message index into a new take ID.
-- [ ] Task: Implement backend logic to promote a specific take ID into an independent, top-level session.
-- [ ] Task: Conductor - User Manual Verification 'Phase 1: Backend Support for Timeline Branching' (Protocol in workflow.md)
+## Phase 1: Backend Support for Timeline Branching [checkpoint: 4039589]
+- [x] Task: Write failing tests for extending the session state model to support branching (tree-like history or parallel linear "takes" with a shared ancestor). [fefa06b]
+- [x] Task: Implement backend logic to branch a session history at a specific message index into a new take ID. [fefa06b]
+- [x] Task: Implement backend logic to promote a specific take ID into an independent, top-level session. [fefa06b]
+- [x] Task: Conductor - User Manual Verification 'Phase 1: Backend Support for Timeline Branching' (Protocol in workflow.md)
 
-## Phase 2: GUI Implementation for Tabbed Takes
-- [ ] Task: Write GUI tests verifying the rendering and navigation of multiple tabs for a single session.
-- [ ] Task: Implement a tabbed interface within the Discussion window to switch between different takes of the active session.
-- [ ] Task: Add a "Split/Branch from here" action to individual message entries in the discussion history.
-- [ ] Task: Add a UI button/action to promote the currently active take to a new separate session.
-- [ ] Task: Conductor - User Manual Verification 'Phase 2: GUI Implementation for Tabbed Takes' (Protocol in workflow.md)
+## Phase 2: GUI Implementation for Tabbed Takes [checkpoint: 9c67ee7]
+- [x] Task: Write GUI tests verifying the rendering and navigation of multiple tabs for a single session. [3225125]
+- [x] Task: Implement a tabbed interface within the Discussion window to switch between different takes of the active session. [3225125]
+- [x] Task: Add a "Split/Branch from here" action to individual message entries in the discussion history. [e48835f]
+- [x] Task: Add a UI button/action to promote the currently active take to a new separate session. [1f7880a]
+- [x] Task: Conductor - User Manual Verification 'Phase 2: GUI Implementation for Tabbed Takes' (Protocol in workflow.md)
 
-## Phase 3: Synthesis Workflow Formatting
-- [ ] Task: Write tests for a new text formatting utility that takes multiple history sequences and generates a compressed, diff-like text representation.
-- [ ] Task: Implement the sequence differencing and compression logic to clearly highlight variances between takes.
-- [ ] Task: Conductor - User Manual Verification 'Phase 3: Synthesis Workflow Formatting' (Protocol in workflow.md)
+## Phase 3: Synthesis Workflow Formatting [checkpoint: f0b8f7d]
+- [x] Task: Write tests for a new text formatting utility that takes multiple history sequences and generates a compressed, diff-like text representation. [510527c]
+- [x] Task: Implement the sequence differencing and compression logic to clearly highlight variances between takes. [510527c]
+- [x] Task: Conductor - User Manual Verification 'Phase 3: Synthesis Workflow Formatting' (Protocol in workflow.md)
 
-## Phase 4: Synthesis UI & Agent Integration
-- [ ] Task: Write GUI tests for the multi-take selection interface and synthesis action.
-- [ ] Task: Implement a UI mechanism allowing users to select multiple takes and provide a synthesis prompt.
-- [ ] Task: Implement the execution pipeline to feed the compressed differences and user prompt to an AI agent, and route the generated synthesis to a new "take" tab.
-- [ ] Task: Conductor - User Manual Verification 'Phase 4: Synthesis UI & Agent Integration' (Protocol in workflow.md)
+## Phase 4: Synthesis UI & Agent Integration [checkpoint: 253d386]
+- [x] Task: Write GUI tests for the multi-take selection interface and synthesis action. [a452c72]
+- [x] Task: Implement a UI mechanism allowing users to select multiple takes and provide a synthesis prompt. [a452c72]
+- [x] Task: Implement the execution pipeline to feed the compressed differences and user prompt to an AI agent, and route the generated synthesis to a new "take" tab. [a452c72]
+- [x] Task: Conductor - User Manual Verification 'Phase 4: Synthesis UI & Agent Integration' (Protocol in workflow.md)
+
+## Phase: Review Fixes
+- [x] Task: Apply review suggestions [2a8af5f]

conductor/tracks/session_context_snapshots_20260311/plan.md

@@ -1,24 +1,24 @@
 # Implementation Plan: Session Context Snapshots & Visibility
 
 ## Phase 1: Backend Support for Context Presets
-- [ ] Task: Write failing tests for saving, loading, and listing Context Presets in the project configuration.
-- [ ] Task: Implement Context Preset storage logic (e.g., updating TOML schemas in `project_manager.py`) to manage file/screenshot lists.
-- [ ] Task: Conductor - User Manual Verification 'Phase 1: Backend Support for Context Presets' (Protocol in workflow.md)
+- [x] Task: Write failing tests for saving, loading, and listing Context Presets in the project configuration. 93a590c
+- [x] Task: Implement Context Preset storage logic (e.g., updating TOML schemas in `project_manager.py`) to manage file/screenshot lists. 93a590c
+- [x] Task: Conductor - User Manual Verification 'Phase 1: Backend Support for Context Presets' (Protocol in workflow.md) 93a590c
 
 ## Phase 2: GUI Integration & Persona Assignment
-- [ ] Task: Write tests for the Context Hub UI components handling preset saving and loading.
-- [ ] Task: Implement the UI controls in the Context Hub to save current selections as a preset and load existing presets.
-- [ ] Task: Update the Persona configuration UI (`personas.py` / `gui_2.py`) to allow assigning a named Context Preset to an agent persona.
-- [ ] Task: Conductor - User Manual Verification 'Phase 2: GUI Integration & Persona Assignment' (Protocol in workflow.md)
+- [x] Task: Write tests for the Context Hub UI components handling preset saving and loading. 573f5ee
+- [x] Task: Implement the UI controls in the Context Hub to save current selections as a preset and load existing presets. 573f5ee
+- [x] Task: Update the Persona configuration UI (`personas.py` / `gui_2.py`) to allow assigning a named Context Preset to an agent persona. 791e1b7
+- [x] Task: Conductor - User Manual Verification 'Phase 2: GUI Integration & Persona Assignment' (Protocol in workflow.md) 791e1b7
 
 ## Phase 3: Transparent Context Visibility
-- [ ] Task: Write tests to ensure the initial aggregate markdown, resolved system prompt, and file injection timestamps are accurately recorded in the session state.
-- [ ] Task: Implement UI elements in the Session Hub to expose the aggregated markdown and the active system prompt.
-- [ ] Task: Enhance the discussion timeline rendering in `gui_2.py` to visually indicate exactly when files and screenshots were injected into the context.
-- [ ] Task: Conductor - User Manual Verification 'Phase 3: Transparent Context Visibility' (Protocol in workflow.md)
+- [x] Task: Write tests to ensure the initial aggregate markdown, resolved system prompt, and file injection timestamps are accurately recorded in the session state. 84b6266
+- [x] Task: Implement UI elements in the Session Hub to expose the aggregated markdown and the active system prompt. 84b6266
+- [x] Task: Enhance the discussion timeline rendering in `gui_2.py` to visually indicate exactly when files and screenshots were injected into the context. 84b6266
+- [x] Task: Conductor - User Manual Verification 'Phase 3: Transparent Context Visibility' (Protocol in workflow.md) 84b6266
 
 ## Phase 4: Agent-Focused Session Filtering
-- [ ] Task: Write tests for the GUI state filtering logic when focusing on a specific agent's session.
-- [ ] Task: Relocate the 'Focus Agent' feature from the Operations Hub to the MMA Dashboard.
-- [ ] Task: Implement the action to filter the Session and Discussion hubs based on the selected agent's context.
-- [ ] Task: Conductor - User Manual Verification 'Phase 4: Agent-Focused Session Filtering' (Protocol in workflow.md)
+- [x] Task: Write tests for the GUI state filtering logic when focusing on a specific agent's session. 038c909
+- [x] Task: Relocate the 'Focus Agent' feature from the Operations Hub to the MMA Dashboard. 038c909
+- [x] Task: Implement the action to filter the Session and Discussion hubs based on the selected agent's context. 038c909
+- [x] Task: Conductor - User Manual Verification 'Phase 4: Agent-Focused Session Filtering' (Protocol in workflow.md) 038c909

conductor/tracks/system_context_exposure_20260322/metadata.json

@@ -0,0 +1,16 @@
+{
+  "name": "system_context_exposure",
+  "created": "2026-03-22",
+  "status": "future",
+  "priority": "medium",
+  "affected_files": [
+    "src/ai_client.py",
+    "src/gui_2.py",
+    "src/models.py"
+  ],
+  "related_tracks": [
+    "discussion_hub_panel_reorganization (in_progress)",
+    "aggregation_smarter_summaries (future)"
+  ],
+  "notes": "Deferred from discussion_hub_panel_reorganization planning. The _SYSTEM_PROMPT in ai_client.py is hidden from users - this exposes it for customization."
+}

conductor/tracks/system_context_exposure_20260322/plan.md

@@ -0,0 +1,41 @@
+# Implementation Plan: System Context Exposure
+
+## Phase 1: Backend Changes
+Focus: Make _SYSTEM_PROMPT configurable
+
+- [ ] Task: Audit ai_client.py system prompt flow
+- [ ] Task: Move _SYSTEM_PROMPT to configurable storage
+- [ ] Task: Implement load/save of base system prompt
+- [ ] Task: Modify _get_combined_system_prompt() to use config
+- [ ] Task: Write tests for configurable system prompt
+- [ ] Task: Conductor - User Manual Verification 'Phase 1: Backend Changes'
+
+## Phase 2: UI Implementation
+Focus: Add base prompt editor to AI Settings
+
+- [ ] Task: Add UI controls to _render_system_prompts_panel
+- [ ] Task: Implement checkbox for "Use Default Base"
+- [ ] Task: Implement collapsible base prompt editor
+- [ ] Task: Add "Reset to Default" button
+- [ ] Task: Write tests for UI controls
+- [ ] Task: Conductor - User Manual Verification 'Phase 2: UI Implementation'
+
+## Phase 3: Persistence & Provider Testing
+Focus: Ensure persistence and cross-provider compatibility
+
+- [ ] Task: Verify base prompt persists across app restarts
+- [ ] Task: Test with Gemini provider
+- [ ] Task: Test with Anthropic provider
+- [ ] Task: Test with DeepSeek provider
+- [ ] Task: Test with Gemini CLI adapter
+- [ ] Task: Conductor - User Manual Verification 'Phase 3: Persistence & Provider Testing'
+
+## Phase 4: Safety & Defaults
+Focus: Ensure users can recover from bad edits
+
+- [ ] Task: Implement confirmation dialog before saving custom base
+- [ ] Task: Add validation for empty/invalid prompts
+- [ ] Task: Document the base prompt purpose in UI
+- [ ] Task: Add "Show Diff" between default and custom
+- [ ] Task: Write tests for safety features
+- [ ] Task: Conductor - User Manual Verification 'Phase 4: Safety & Defaults'

conductor/tracks/system_context_exposure_20260322/spec.md

@@ -0,0 +1,120 @@
+# Specification: System Context Exposure
+
+## 1. Overview
+
+This track exposes the hidden system prompt from `ai_client.py` to users for customization.
+
+**Current Problem:**
+- `_SYSTEM_PROMPT` in `ai_client.py` (lines ~118-143) is hardcoded
+- It contains foundational instructions: "You are a helpful coding assistant with access to a PowerShell tool..."
+- Users can only see/appending their custom portion via `_custom_system_prompt`
+- The base prompt that defines core agent capabilities is invisible
+
+**Goal:**
+- Make `_SYSTEM_PROMPT` visible and editable in the UI
+- Allow users to customize the foundational agent instructions
+- Maintain sensible defaults while enabling expert customization
+
+## 2. Current State Audit
+
+### Hidden System Prompt Location
+`src/ai_client.py`:
+```python
+_SYSTEM_PROMPT: str = (
+ "You are a helpful coding assistant with access to a PowerShell tool (run_powershell) and MCP tools (file access: read_file, list_directory, search_files, get_file_summary, web access: web_search, fetch_url). "
+ "When calling file/directory tools, always use the 'path' parameter for the target path. "
+ ...
+)
+```
+
+### Related State
+- `_custom_system_prompt` - user-defined append/injection
+- `_get_combined_system_prompt()` - merges both
+- `set_custom_system_prompt()` - setter for user portion
+
+### UI Current State
+- AI Settings → System Prompts shows global and project prompts
+- These are injected as `[USER SYSTEM PROMPT]` after `_SYSTEM_PROMPT`
+- But `_SYSTEM_PROMPT` itself is never shown
+
+## 3. Functional Requirements
+
+### 3.1 Base System Prompt Visibility
+- Add "Base System Prompt" section in AI Settings
+- Display current `_SYSTEM_PROMPT` content
+- Allow editing with syntax highlighting (it's markdown text)
+
+### 3.2 Default vs Custom Base
+- Maintain default base prompt as reference
+- User can reset to default if they mess it up
+- Show diff between default and custom
+
+### 3.3 Persistence
+- Custom base prompt stored in config or project TOML
+- Loaded on app start
+- Applied before `_custom_system_prompt` in `_get_combined_system_prompt()`
+
+### 3.4 Provider Considerations
+- Some providers handle system prompts differently
+- Verify behavior across Gemini, Anthropic, DeepSeek
+- May need provider-specific base prompts
+
+## 4. Data Model
+
+### 4.1 Config Storage
+```toml
+[ai_settings]
+base_system_prompt = """..."""
+use_default_base = true
+```
+
+### 4.2 Combined Prompt Order
+1. `_SYSTEM_PROMPT` (or custom base if enabled)
+2. `[USER SYSTEM PROMPT]` (from AI Settings global/project)
+3. Tooling strategy (from bias engine)
+
+## 5. UI Design
+
+**Location:** AI Settings panel → System Prompts section
+
+```
+┌─ System Prompts ──────────────────────────────┐
+│ ☑ Use Default Base System Prompt              │
+│                                              │
+│ Base System Prompt (collapsed by default):    │
+│ ┌──────────────────────────────────────────┐ │
+│ │ You are a helpful coding assistant...     │ │
+│ └──────────────────────────────────────────┘ │
+│                                              │
+│ [Show Editor] [Reset to Default]              │
+│                                              │
+│ Global System Prompt:                         │
+│ ┌──────────────────────────────────────────┐ │
+│ │ [current global prompt content]           │ │
+│ └──────────────────────────────────────────┘ │
+└──────────────────────────────────────────────┘
+```
+
+When "Show Editor" clicked:
+- Expand to full editor for base prompt
+- Syntax highlighting for markdown
+- Character count
+
+## 6. Acceptance Criteria
+
+- [ ] `_SYSTEM_PROMPT` visible in AI Settings
+- [ ] User can edit base system prompt
+- [ ] Changes persist across app restarts
+- [ ] "Reset to Default" restores original
+- [ ] Provider APIs receive modified prompt correctly
+- [ ] No regression in agent behavior with defaults
+
+## 7. Out of Scope
+- Changes to actual agent behavior logic
+- Changes to tool definitions or availability
+- Changes to aggregation or context handling
+
+## 8. Dependencies
+- `ai_client.py` - `_SYSTEM_PROMPT` and `_get_combined_system_prompt()`
+- `gui_2.py` - AI Settings panel rendering
+- `models.py` - Config structures

conductor/tracks/text_viewer_rich_rendering_20260313/plan.md

@@ -1,29 +1,29 @@
 # Implementation Plan: Advanced Text Viewer with Syntax Highlighting
 
 ## Phase 1: State & Interface Update
-- [ ] Task: Audit `src/gui_2.py` to ensure all `text_viewer_*` state variables are explicitly initialized in `App.__init__`.
-- [ ] Task: Implement: Update `App.__init__` to initialize `self.show_text_viewer`, `self.text_viewer_title`, `self.text_viewer_content`, and new `self.text_viewer_type` (defaulting to "text").
-- [ ] Task: Implement: Update `self.text_viewer_wrap` (defaulting to True) to allow independent word wrap.
-- [ ] Task: Implement: Update `_render_text_viewer(self, label: str, content: str, text_type: str = "text")` signature and caller usage.
-- [ ] Task: Conductor - User Manual Verification 'Phase 1: State & Interface Update' (Protocol in workflow.md)
+- [x] Task: Audit `src/gui_2.py` to ensure all `text_viewer_*` state variables are explicitly initialized in `App.__init__`. e28af48
+- [x] Task: Implement: Update `App.__init__` to initialize `self.show_text_viewer`, `self.text_viewer_title`, `self.text_viewer_content`, and new `self.text_viewer_type` (defaulting to "text"). e28af48
+- [x] Task: Implement: Update `self.text_viewer_wrap` (defaulting to True) to allow independent word wrap. e28af48
+- [x] Task: Implement: Update `_render_text_viewer(self, label: str, content: str, text_type: str = "text")` signature and caller usage. e28af48
+- [x] Task: Conductor - User Manual Verification 'Phase 1: State & Interface Update' (Protocol in workflow.md) e28af48
 
 ## Phase 2: Core Rendering Logic (Code & MD)
-- [ ] Task: Write Tests: Create a simulation test in `tests/test_gui_text_viewer.py` to verify the viewer opens and switches rendering paths based on `text_type`.
-- [ ] Task: Implement: In `src/gui_2.py`, refactor the text viewer window loop to:
-  - Use `MarkdownRenderer.render` if `text_type == "markdown"`.
-  - Use a cached `ImGuiColorTextEdit.TextEditor` if `text_type` matches a code language.
-  - Fallback to `imgui.input_text_multiline` for plain text.
-- [ ] Task: Implement: Ensure the `TextEditor` instance is properly cached using a unique key for the text viewer to maintain state.
-- [ ] Task: Conductor - User Manual Verification 'Phase 2: Core Rendering Logic' (Protocol in workflow.md)
+- [x] Task: Write Tests: Create a simulation test in `tests/test_gui_text_viewer.py` to verify the viewer opens and switches rendering paths based on `text_type`. a91b8dc
+- [x] Task: Implement: In `src/gui_2.py`, refactor the text viewer window loop to: a91b8dc
+  - Use `MarkdownRenderer.render` if `text_type == "markdown"`. a91b8dc
+  - Use a cached `ImGuiColorTextEdit.TextEditor` if `text_type` matches a code language. a91b8dc
+  - Fallback to `imgui.input_text_multiline` for plain text. a91b8dc
+- [x] Task: Implement: Ensure the `TextEditor` instance is properly cached using a unique key for the text viewer to maintain state. a91b8dc
+- [x] Task: Conductor - User Manual Verification 'Phase 2: Core Rendering Logic' (Protocol in workflow.md) a91b8dc
 
 ## Phase 3: UI Features (Copy, Line Numbers, Wrap)
-- [ ] Task: Write Tests: Update `tests/test_gui_text_viewer.py` to verify the copy-to-clipboard functionality and word wrap toggle.
-- [ ] Task: Implement: Add a "Copy" button to the text viewer title bar or a small toolbar at the top of the window.
-- [ ] Task: Implement: Add a "Word Wrap" checkbox inside the text viewer window.
-- [ ] Task: Implement: Configure the `TextEditor` instance to show line numbers and be read-only.
-- [ ] Task: Conductor - User Manual Verification 'Phase 3: UI Features' (Protocol in workflow.md)
+- [x] Task: Write Tests: Update `tests/test_gui_text_viewer.py` to verify the copy-to-clipboard functionality and word wrap toggle. a91b8dc
+- [x] Task: Implement: Add a "Copy" button to the text viewer title bar or a small toolbar at the top of the window. a91b8dc
+- [x] Task: Implement: Add a "Word Wrap" checkbox inside the text viewer window. a91b8dc
+- [x] Task: Implement: Configure the `TextEditor` instance to show line numbers and be read-only. a91b8dc
+- [x] Task: Conductor - User Manual Verification 'Phase 3: UI Features' (Protocol in workflow.md) a91b8dc
 
 ## Phase 4: Integration & Rollout
-- [ ] Task: Implement: Update all existing calls to `_render_text_viewer` in `src/gui_2.py` (e.g., in `_render_files_panel`, `_render_tool_calls_panel`) to pass the correct `text_type` based on file extension or content.
-- [ ] Task: Implement: Add "Markdown Preview" support for system prompt presets using the new text viewer logic.
-- [ ] Task: Conductor - User Manual Verification 'Phase 4: Integration & Rollout' (Protocol in workflow.md)
+- [x] Task: Implement: Update all existing calls to `_render_text_viewer` in `src/gui_2.py` (e.g., in `_render_files_panel`, `_render_tool_calls_panel`) to pass the correct `text_type` based on file extension or content. 2826ad5
+- [x] Task: Implement: Add "Markdown Preview" support for system prompt presets using the new text viewer logic. 2826ad5
+- [x] Task: Conductor - User Manual Verification 'Phase 4: Integration & Rollout' (Protocol in workflow.md) 2826ad5

conductor/tracks/thinking_trace_handling_20260313/plan.md

@@ -1,26 +1,23 @@
 # Implementation Plan: Rich Thinking Trace Handling
 
-## Phase 1: Core Parsing & Model Update
-- [ ] Task: Audit `src/models.py` and `src/project_manager.py` to identify current message serialization schemas.
-- [ ] Task: Write Tests: Verify that raw AI responses with `<thinking>`, `<thought>`, and `Thinking:` markers are correctly parsed into segmented data structures (Thinking vs. Response).
-- [ ] Task: Implement: Add `ThinkingSegment` model and update `ChatMessage` schema in `src/models.py` to support optional thinking traces.
-- [ ] Task: Implement: Update parsing logic in `src/ai_client.py` or a dedicated utility to extract segments from raw provider responses.
-- [ ] Task: Conductor - User Manual Verification 'Phase 1: Core Parsing & Model Update' (Protocol in workflow.md)
+## Status: COMPLETE (2026-03-14)
 
-## Phase 2: Persistence & History Integration
-- [ ] Task: Write Tests: Verify that `ProjectManager` correctly serializes and deserializes messages with thinking segments to/from TOML history files.
-- [ ] Task: Implement: Update `src/project_manager.py` to handle the new `ChatMessage` schema during session save/load.
-- [ ] Task: Implement: Ensure `src/aggregate.py` or relevant context builders include thinking traces in the "Discussion History" sent back to the AI.
-- [ ] Task: Conductor - User Manual Verification 'Phase 2: Persistence & History Integration' (Protocol in workflow.md)
+## Summary
+Implemented thinking trace parsing, model, persistence, and GUI rendering for AI responses containing `<thinking>`, `<thought>`, and `Thinking:` markers.
 
-## Phase 3: GUI Rendering - Comms & Discussion
-- [ ] Task: Write Tests: Verify the GUI rendering logic correctly handles messages with and without thinking segments.
-- [ ] Task: Implement: Create a reusable `_render_thinking_trace` helper in `src/gui_2.py` using a collapsible header (e.g., `imgui.collapsing_header`).
-- [ ] Task: Implement: Integrate the thinking trace renderer into the **Comms History** panel in `src/gui_2.py`.
-- [ ] Task: Implement: Integrate the thinking trace renderer into the **Discussion Hub** message loop in `src/gui_2.py`.
-- [ ] Task: Conductor - User Manual Verification 'Phase 3: GUI Rendering - Comms & Discussion' (Protocol in workflow.md)
+## Files Created/Modified:
+- `src/thinking_parser.py` - Parser for thinking traces
+- `src/models.py` - ThinkingSegment model
+- `src/gui_2.py` - _render_thinking_trace helper + integration
+- `tests/test_thinking_trace.py` - 7 parsing tests
+- `tests/test_thinking_persistence.py` - 4 persistence tests  
+- `tests/test_thinking_gui.py` - 4 GUI tests
 
-## Phase 4: Final Polish & Theming
-- [ ] Task: Implement: Apply specialized styling (e.g., tinted background or italicized text) to expanded thinking traces to distinguish them from direct responses.
-- [ ] Task: Implement: Ensure thinking trace headers show a "Calculating..." or "Monologue" indicator while an agent is active.
-- [ ] Task: Conductor - User Manual Verification 'Phase 4: Final Polish & Theming' (Protocol in workflow.md)
+## Implementation Details:
+- **Parser**: Extracts thinking segments from `<thinking>`, `<thought>`, `Thinking:` markers
+- **Model**: `ThinkingSegment` dataclass with content and marker fields
+- **GUI**: `_render_thinking_trace` with collapsible "Monologue" header
+- **Styling**: Tinted background (dark brown), gold/amber text
+- **Indicator**: Existing "THINKING..." in Discussion Hub
+
+## Total Tests: 15 passing

config.toml

@@ -5,25 +5,20 @@ temperature = 0.0
 top_p = 1.0
 max_tokens = 32000
 history_trunc_limit = 900000
-active_preset = "Default"
-system_prompt = ""
+active_preset = ""
+system_prompt = "Overridden Prompt"
 
 [projects]
 paths = [
-    "C:/projects/gencpp/gencpp_sloppy.toml",
-    "C:\\projects\\manual_slop\\tests\\artifacts\\temp_livecontextsim.toml",
-    "C:\\projects\\manual_slop\\tests\\artifacts\\temp_liveaisettingssim.toml",
-    "C:\\projects\\manual_slop\\tests\\artifacts\\temp_livetoolssim.toml",
-    "C:\\projects\\manual_slop\\tests\\artifacts\\temp_liveexecutionsim.toml",
-    "C:\\projects\\manual_slop\\tests\\artifacts\\temp_project.toml",
+    "C:/projects/gencpp/.ai/gencpp_sloppy.toml",
 ]
-active = "C:/projects/gencpp/gencpp_sloppy.toml"
+active = "C:/projects/gencpp/.ai/gencpp_sloppy.toml"
 
 [gui]
 separate_message_panel = false
 separate_response_panel = false
 separate_tool_calls_panel = false
-bg_shader_enabled = true
+bg_shader_enabled = false
 crt_filter_enabled = false
 separate_task_dag = false
 separate_usage_analytics = false
@@ -34,12 +29,12 @@ separate_tier4 = false
 separate_external_tools = false
 
 [gui.show_windows]
-"Context Hub" = true
+"Project Settings" = true
 "Files & Media" = true
 "AI Settings" = true
-"MMA Dashboard" = true
-"Task DAG" = false
-"Usage Analytics" = false
+"MMA Dashboard" = false
+"Task DAG" = true
+"Usage Analytics" = true
 "Tier 1" = false
 "Tier 2" = false
 "Tier 3" = false
@@ -51,21 +46,22 @@ separate_external_tools = false
 "Discussion Hub" = true
 "Operations Hub" = true
 Message = false
-Response = true
+Response = false
 "Tool Calls" = false
-Theme = true
-"Log Management" = true
+Theme = false
+"Log Management" = false
 Diagnostics = false
 "External Tools" = false
 "Shader Editor" = false
+"Session Hub" = false
 
 [theme]
 palette = "Nord Dark"
-font_path = "C:/projects/manual_slop/assets/fonts/MapleMono-Regular.ttf"
-font_size = 18.0
+font_path = "fonts/Inter-Regular.ttf"
+font_size = 16.0
 scale = 1.0
-transparency = 0.5400000214576721
-child_transparency = 0.5899999737739563
+transparency = 1.0
+child_transparency = 1.0
 
 [mma]
 max_workers = 4

manualslop_layout.ini

@@ -12,7 +12,7 @@ ViewportPos=43,95
 ViewportId=0x78C57832
 Size=897,649
 Collapsed=0
-DockId=0x00000001,0
+DockId=0x00000005,0
 
 [Window][Files]
 ViewportPos=3125,170
@@ -33,7 +33,7 @@ DockId=0x0000000A,0
 Pos=0,17
 Size=1680,730
 Collapsed=0
-DockId=0x00000001,0
+DockId=0x00000005,0
 
 [Window][Provider]
 ViewportPos=43,95
@@ -41,23 +41,23 @@ ViewportId=0x78C57832
 Pos=0,651
 Size=897,468
 Collapsed=0
-DockId=0x00000001,0
+DockId=0x00000005,0
 
 [Window][Message]
-Pos=661,1426
+Pos=711,694
 Size=716,455
 Collapsed=0
 
 [Window][Response]
-Pos=2437,925
-Size=1111,773
+Pos=245,1014
+Size=1492,948
 Collapsed=0
 
 [Window][Tool Calls]
-Pos=520,1144
-Size=663,232
+Pos=1028,1668
+Size=1397,340
 Collapsed=0
-DockId=0x00000006,0
+DockId=0x0000000E,0
 
 [Window][Comms History]
 ViewportPos=43,95
@@ -74,10 +74,10 @@ Collapsed=0
 DockId=0xAFC85805,2
 
 [Window][Theme]
-Pos=0,703
-Size=630,737
+Pos=0,975
+Size=1010,730
 Collapsed=0
-DockId=0x00000002,2
+DockId=0x00000007,0
 
 [Window][Text Viewer - Entry #7]
 Pos=379,324
@@ -85,16 +85,15 @@ Size=900,700
 Collapsed=0
 
 [Window][Diagnostics]
-Pos=1649,24
-Size=580,1284
+Pos=1945,734
+Size=1211,713
 Collapsed=0
-DockId=0x00000010,2
 
 [Window][Context Hub]
-Pos=0,703
-Size=630,737
+Pos=0,975
+Size=1010,730
 Collapsed=0
-DockId=0x00000002,1
+DockId=0x00000007,0
 
 [Window][AI Settings Hub]
 Pos=406,17
@@ -103,28 +102,28 @@ Collapsed=0
 DockId=0x0000000D,0
 
 [Window][Discussion Hub]
-Pos=1263,22
-Size=709,1418
+Pos=1126,24
+Size=1638,1608
 Collapsed=0
-DockId=0x00000013,0
+DockId=0x00000006,0
 
 [Window][Operations Hub]
-Pos=632,22
-Size=629,1418
+Pos=0,24
+Size=1124,1608
 Collapsed=0
-DockId=0x00000005,0
+DockId=0x00000005,2
 
 [Window][Files & Media]
-Pos=0,703
-Size=630,737
+Pos=1126,24
+Size=1638,1608
 Collapsed=0
-DockId=0x00000002,0
+DockId=0x00000006,1
 
 [Window][AI Settings]
-Pos=0,22
-Size=630,679
+Pos=0,24
+Size=1124,1608
 Collapsed=0
-DockId=0x00000001,0
+DockId=0x00000005,0
 
 [Window][Approve Tool Execution]
 Pos=3,524
@@ -132,16 +131,16 @@ Size=416,325
 Collapsed=0
 
 [Window][MMA Dashboard]
-Pos=1974,22
-Size=586,1418
+Pos=3360,26
+Size=480,2134
 Collapsed=0
-DockId=0x00000010,0
+DockId=0x00000004,0
 
 [Window][Log Management]
-Pos=1974,22
-Size=586,1418
+Pos=3360,26
+Size=480,2134
 Collapsed=0
-DockId=0x00000010,1
+DockId=0x00000004,0
 
 [Window][Track Proposal]
 Pos=709,326
@@ -175,8 +174,8 @@ Size=381,329
 Collapsed=0
 
 [Window][Last Script Output]
-Pos=2810,265
-Size=800,562
+Pos=1076,794
+Size=1085,1154
 Collapsed=0
 
 [Window][Text Viewer - Log Entry #1 (request)]
@@ -190,7 +189,7 @@ Size=1005,366
 Collapsed=0
 
 [Window][Text Viewer - Entry #11]
-Pos=60,60
+Pos=1010,564
 Size=1529,925
 Collapsed=0
 
@@ -220,13 +219,13 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - text]
-Pos=60,60
+Pos=1297,550
 Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - system]
-Pos=377,705
-Size=900,340
+Pos=901,1502
+Size=876,536
 Collapsed=0
 
 [Window][Text Viewer - Entry #15]
@@ -240,8 +239,8 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - tool_calls]
-Pos=60,60
-Size=900,700
+Pos=1106,942
+Size=831,482
 Collapsed=0
 
 [Window][Text Viewer - Tool Script #1]
@@ -285,7 +284,7 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - Tool Call #1 Details]
-Pos=165,1081
+Pos=963,716
 Size=727,725
 Collapsed=0
 
@@ -330,8 +329,8 @@ Size=967,499
 Collapsed=0
 
 [Window][Usage Analytics]
-Pos=1739,1107
-Size=586,269
+Pos=2678,26
+Size=1162,2134
 Collapsed=0
 DockId=0x0000000F,0
 
@@ -366,7 +365,7 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - Entry #4]
-Pos=1127,922
+Pos=1165,782
 Size=900,700
 Collapsed=0
 
@@ -376,15 +375,42 @@ Size=1593,1240
 Collapsed=0
 
 [Window][Text Viewer - Entry #5]
-Pos=60,60
-Size=900,700
+Pos=989,778
+Size=1366,1032
 Collapsed=0
 
 [Window][Shader Editor]
 Pos=457,710
-Size=493,252
+Size=573,280
 Collapsed=0
 
+[Window][Text Viewer - list_directory]
+Pos=1376,796
+Size=882,656
+Collapsed=0
+
+[Window][Text Viewer - Last Output]
+Pos=60,60
+Size=900,700
+Collapsed=0
+
+[Window][Text Viewer - Entry #2]
+Pos=1518,488
+Size=900,700
+Collapsed=0
+
+[Window][Session Hub]
+Pos=1163,24
+Size=1234,1542
+Collapsed=0
+DockId=0x00000006,1
+
+[Window][Project Settings]
+Pos=0,24
+Size=1124,1608
+Collapsed=0
+DockId=0x00000005,1
+
 [Table][0xFB6E3870,4]
 RefScale=13
 Column 0  Width=80
@@ -418,9 +444,9 @@ Column 4  Weight=1.0000
 [Table][0x2A6000B6,4]
 RefScale=16
 Column 0  Width=48
-Column 1  Width=68
+Column 1  Width=67
 Column 2  Weight=1.0000
-Column 3  Width=120
+Column 3  Width=243
 
 [Table][0x8BCC69C7,6]
 RefScale=13
@@ -432,17 +458,17 @@ Column 4  Weight=1.0000
 Column 5  Width=50
 
 [Table][0x3751446B,4]
-RefScale=16
-Column 0  Width=48
-Column 1  Width=72
+RefScale=18
+Column 0  Width=54
+Column 1  Width=81
 Column 2  Weight=1.0000
-Column 3  Width=120
+Column 3  Width=135
 
 [Table][0x2C515046,4]
 RefScale=16
 Column 0  Width=48
 Column 1  Weight=1.0000
-Column 2  Width=118
+Column 2  Width=166
 Column 3  Width=48
 
 [Table][0xD99F45C5,4]
@@ -465,7 +491,7 @@ Column 2  Weight=1.0000
 
 [Table][0xA02D8C87,3]
 RefScale=16
-Column 0  Width=180
+Column 0  Width=179
 Column 1  Width=120
 Column 2  Weight=1.0000
 
@@ -480,13 +506,13 @@ Column 0  Width=150
 Column 1  Weight=1.0000
 
 [Table][0x8D8494AB,2]
-RefScale=16
-Column 0  Width=132
+RefScale=18
+Column 0  Width=148
 Column 1  Weight=1.0000
 
 [Table][0x2C261E6E,2]
-RefScale=16
-Column 0  Width=99
+RefScale=18
+Column 0  Width=111
 Column 1  Weight=1.0000
 
 [Table][0x9CB1E6FD,2]
@@ -495,26 +521,20 @@ Column 0  Width=187
 Column 1  Weight=1.0000
 
 [Docking][Data]
-DockNode            ID=0x00000008 Pos=3125,170 Size=593,1157 Split=Y
-  DockNode          ID=0x00000009 Parent=0x00000008 SizeRef=1029,147 Selected=0x0469CA7A
-  DockNode          ID=0x0000000A Parent=0x00000008 SizeRef=1029,145 Selected=0xDF822E02
-DockSpace           ID=0xAFC85805 Window=0x079D3A04 Pos=0,22 Size=2560,1418 Split=X
-  DockNode          ID=0x00000003 Parent=0xAFC85805 SizeRef=1640,1183 Split=X
-    DockNode        ID=0x0000000B Parent=0x00000003 SizeRef=404,1186 Split=X Selected=0xF4139CA2
-      DockNode      ID=0x00000007 Parent=0x0000000B SizeRef=630,858 Split=Y Selected=0x8CA2375C
-        DockNode    ID=0x00000001 Parent=0x00000007 SizeRef=824,525 CentralNode=1 Selected=0x7BD57D6A
-        DockNode    ID=0x00000002 Parent=0x00000007 SizeRef=824,737 Selected=0x8CA2375C
-      DockNode      ID=0x0000000E Parent=0x0000000B SizeRef=1340,858 Split=X Selected=0x418C7449
-        DockNode    ID=0x00000012 Parent=0x0000000E SizeRef=629,402 Split=Y Selected=0x418C7449
-          DockNode  ID=0x00000005 Parent=0x00000012 SizeRef=876,1749 Selected=0x418C7449
-          DockNode  ID=0x00000006 Parent=0x00000012 SizeRef=876,362 Selected=0x1D56B311
-        DockNode    ID=0x00000013 Parent=0x0000000E SizeRef=709,402 Selected=0x6F2B5B04
-    DockNode        ID=0x0000000D Parent=0x00000003 SizeRef=435,1186 Selected=0x363E93D6
-  DockNode          ID=0x00000004 Parent=0xAFC85805 SizeRef=586,1183 Split=Y Selected=0x3AEC3498
-    DockNode        ID=0x00000010 Parent=0x00000004 SizeRef=1199,1689 Selected=0x2C0206CE
-    DockNode        ID=0x00000011 Parent=0x00000004 SizeRef=1199,420 Split=X Selected=0xDEB547B6
-      DockNode      ID=0x0000000C Parent=0x00000011 SizeRef=916,380 Selected=0x655BC6E9
-      DockNode      ID=0x0000000F Parent=0x00000011 SizeRef=281,380 Selected=0xDEB547B6
+DockNode          ID=0x00000008 Pos=3125,170 Size=593,1157 Split=Y
+  DockNode        ID=0x00000009 Parent=0x00000008 SizeRef=1029,147 Selected=0x0469CA7A
+  DockNode        ID=0x0000000A Parent=0x00000008 SizeRef=1029,145 Selected=0xDF822E02
+DockSpace         ID=0xAFC85805 Window=0x079D3A04 Pos=0,24 Size=2764,1608 Split=X
+  DockNode        ID=0x00000003 Parent=0xAFC85805 SizeRef=2175,1183 Split=X
+    DockNode      ID=0x0000000B Parent=0x00000003 SizeRef=404,1186 Split=X Selected=0xF4139CA2
+      DockNode    ID=0x00000007 Parent=0x0000000B SizeRef=1512,858 Split=X Selected=0x8CA2375C
+        DockNode  ID=0x00000005 Parent=0x00000007 SizeRef=1226,1681 CentralNode=1 Selected=0x7BD57D6A
+        DockNode  ID=0x00000006 Parent=0x00000007 SizeRef=1638,1681 Selected=0x6F2B5B04
+      DockNode    ID=0x0000000E Parent=0x0000000B SizeRef=1777,858 Selected=0x418C7449
+    DockNode      ID=0x0000000D Parent=0x00000003 SizeRef=435,1186 Selected=0x363E93D6
+  DockNode        ID=0x00000004 Parent=0xAFC85805 SizeRef=1162,1183 Split=X Selected=0x3AEC3498
+    DockNode      ID=0x0000000C Parent=0x00000004 SizeRef=916,380 Selected=0x655BC6E9
+    DockNode      ID=0x0000000F Parent=0x00000004 SizeRef=281,380 Selected=0xDEB547B6
 
 ;;;<<<Layout_655921752_Default>>>;;;
 ;;;<<<HelloImGui_Misc>>>;;;

opencode.json

@@ -71,5 +71,6 @@
       "logs/**",
       "*.log"
     ]
-  }
+  },
+  "plugin": ["superpowers@git+https://github.com/obra/superpowers.git"]
 }

project.toml

@@ -17,6 +17,8 @@ paths = []
 base_dir = "."
 paths = []
 
+[context_presets]
+
 [gemini_cli]
 binary_path = "gemini"
 

project_history.toml

@@ -9,5 +9,5 @@ active = "main"
 
 [discussions.main]
 git_commit = ""
-last_updated = "2026-03-12T20:34:43"
+last_updated = "2026-03-22T12:59:02"
 history = []

src/api_hooks.py

@@ -225,6 +225,9 @@ class HookHandler(BaseHTTPRequestHandler):
       for key, attr in gettable.items():
        val = _get_app_attr(app, attr, None)
        result[key] = _serialize_for_api(val)
+      result['show_text_viewer'] = _get_app_attr(app, 'show_text_viewer', False)
+      result['text_viewer_title'] = _get_app_attr(app, 'text_viewer_title', '')
+      result['text_viewer_type'] = _get_app_attr(app, 'text_viewer_type', 'markdown')
      finally: event.set()
     lock = _get_app_attr(app, "_pending_gui_tasks_lock")
     tasks = _get_app_attr(app, "_pending_gui_tasks")
@@ -250,7 +253,7 @@ class HookHandler(BaseHTTPRequestHandler):
     self.end_headers()
     files = _get_app_attr(app, "files", [])
     screenshots = _get_app_attr(app, "screenshots", [])
-    self.wfile.write(json.dumps({"files": files, "screenshots": screenshots}).encode("utf-8"))
+    self.wfile.write(json.dumps({"files": _serialize_for_api(files), "screenshots": _serialize_for_api(screenshots)}).encode("utf-8"))
    elif self.path == "/api/metrics/financial":
     self.send_response(200)
     self.send_header("Content-Type", "application/json")

src/app_controller.py

@@ -25,6 +25,7 @@ from src import project_manager
 from src import performance_monitor
 from src import models
 from src import presets
+from src import thinking_parser
 from src.file_cache import ASTParser
 from src import ai_client
 from src import shell_runner
@@ -229,7 +230,6 @@ class AppController:
   self.ui_project_system_prompt: str = ""
   self.ui_gemini_cli_path: str = "gemini"
   self.ui_word_wrap: bool = True
-  self.ui_summary_only: bool = False
   self.ui_auto_add_history: bool = False
   self.ui_active_tool_preset: str | None = None
   self.ui_global_system_prompt: str = ""
@@ -242,6 +242,8 @@ class AppController:
   self.ai_status: str = 'idle'
   self.ai_response: str = ''
   self.last_md: str = ''
+  self.last_aggregate_markdown: str = ''
+  self.last_resolved_system_prompt: str = ''
   self.last_md_path: Optional[Path] = None
   self.last_file_items: List[Any] = []
   self.send_thread: Optional[threading.Thread] = None
@@ -251,6 +253,7 @@ class AppController:
   self.show_text_viewer: bool = False
   self.text_viewer_title: str = ''
   self.text_viewer_content: str = ''
+  self.text_viewer_type: str = 'text'
   self._pending_comms: List[Dict[str, Any]] = []
   self._pending_tool_calls: List[Dict[str, Any]] = []
   self._pending_history_adds: List[Dict[str, Any]] = []
@@ -374,7 +377,10 @@ class AppController:
    'ui_separate_tier1': 'ui_separate_tier1',
    'ui_separate_tier2': 'ui_separate_tier2',
    'ui_separate_tier3': 'ui_separate_tier3',
-   'ui_separate_tier4': 'ui_separate_tier4'
+   'ui_separate_tier4': 'ui_separate_tier4',
+   'show_text_viewer': 'show_text_viewer',
+   'text_viewer_title': 'text_viewer_title',
+   'text_viewer_type': 'text_viewer_type'
   }
   self._gettable_fields = dict(self._settable_fields)
   self._gettable_fields.update({
@@ -421,7 +427,10 @@ class AppController:
    'ui_separate_tier1': 'ui_separate_tier1',
    'ui_separate_tier2': 'ui_separate_tier2',
    'ui_separate_tier3': 'ui_separate_tier3',
-   'ui_separate_tier4': 'ui_separate_tier4'
+   'ui_separate_tier4': 'ui_separate_tier4',
+   'show_text_viewer': 'show_text_viewer',
+   'text_viewer_title': 'text_viewer_title',
+   'text_viewer_type': 'text_viewer_type'
   })
   self.perf_monitor = performance_monitor.get_monitor()
   self._perf_profiling_enabled = False
@@ -610,16 +619,6 @@ class AppController:
       self._token_stats_dirty = True
       if not is_streaming:
        self._autofocus_response_tab = True
-      # ONLY add to history when turn is complete
-     if self.ui_auto_add_history and not stream_id and not is_streaming:
-      role = payload.get("role", "AI")
-      with self._pending_history_adds_lock:
-       self._pending_history_adds.append({
-         "role": role, 
-         "content": self.ai_response, 
-         "collapsed": True, 
-         "ts": project_manager.now_ts()
-        })
     elif action in ("mma_stream", "mma_stream_append"):
     # Some events might have these at top level, some in a 'payload' dict
      stream_id = task.get("stream_id") or task.get("payload", {}).get("stream_id")
@@ -912,7 +911,6 @@ class AppController:
   self.ui_gemini_cli_path = self.project.get("gemini_cli", {}).get("binary_path", "gemini")
   self._update_gcli_adapter(self.ui_gemini_cli_path)
   self.ui_word_wrap = proj_meta.get("word_wrap", True)
-  self.ui_summary_only = proj_meta.get("summary_only", False)
   self.ui_auto_add_history = disc_sec.get("auto_add", False)
   self.ui_global_system_prompt = self.config.get("ai", {}).get("system_prompt", "")
   
@@ -952,7 +950,7 @@ class AppController:
   bg_shader.get_bg().enabled = gui_cfg.get("bg_shader_enabled", False)
   
   _default_windows = {
-   "Context Hub": True,
+   "Project Settings": True,
    "Files & Media": True,
    "AI Settings": True,
    "MMA Dashboard": True,
@@ -1467,9 +1465,22 @@ class AppController:
   
   if kind == "response" and "usage" in payload:
    u = payload["usage"]
-   for k in ["input_tokens", "output_tokens", "cache_read_input_tokens", "cache_creation_input_tokens", "total_tokens"]:
-    if k in u:
-     self.session_usage[k] += u.get(k, 0) or 0
+   inp = u.get("input_tokens", u.get("prompt_tokens", 0))
+   out = u.get("output_tokens", u.get("completion_tokens", 0))
+   cache_read = u.get("cache_read_input_tokens", 0)
+   cache_create = u.get("cache_creation_input_tokens", 0)
+   total = u.get("total_tokens", 0)
+
+   # Store normalized usage back in payload for history rendering
+   u["input_tokens"] = inp
+   u["output_tokens"] = out
+   u["cache_read_input_tokens"] = cache_read
+
+   self.session_usage["input_tokens"] += inp
+   self.session_usage["output_tokens"] += out
+   self.session_usage["cache_read_input_tokens"] += cache_read
+   self.session_usage["cache_creation_input_tokens"] += cache_create
+   self.session_usage["total_tokens"] += total
    input_t = u.get("input_tokens", 0)
    output_t = u.get("output_tokens", 0)
    model = payload.get("model", "unknown")
@@ -1490,22 +1501,42 @@ class AppController:
       "ts": entry.get("ts", project_manager.now_ts())
      })
 
-  if kind in ("tool_result", "tool_call"):
-   role = "Tool" if kind == "tool_result" else "Vendor API"
-   content = ""
-   if kind == "tool_result":
-    content = payload.get("output", "")
-   else:
-    content = payload.get("script") or payload.get("args") or payload.get("message", "")
-    if isinstance(content, dict):
-     content = json.dumps(content, indent=1)
-   with self._pending_history_adds_lock:
-    self._pending_history_adds.append({
+  if kind == "response":
+   if self.ui_auto_add_history:
+    role = payload.get("role", "AI")
+    text_content = payload.get("text", "")
+    if text_content.strip():
+     segments, parsed_response = thinking_parser.parse_thinking_trace(text_content)
+     entry_obj = {
       "role": role,
-      "content": f"[{kind.upper().replace('_', ' ')}]\n{content}",
+      "content": parsed_response.strip() if parsed_response else "",
       "collapsed": True,
       "ts": entry.get("ts", project_manager.now_ts())
-     })
+     }
+     if segments:
+      entry_obj["thinking_segments"] = [{"content": s.content, "marker": s.marker} for s in segments]
+     
+     if entry_obj["content"] or segments:
+      with self._pending_history_adds_lock:
+       self._pending_history_adds.append(entry_obj)
+
+  if kind in ("tool_result", "tool_call"):
+   if self.ui_auto_add_history:
+    role = "Tool" if kind == "tool_result" else "Vendor API"
+    content = ""
+    if kind == "tool_result":
+     content = payload.get("output", "")
+    else:
+     content = payload.get("script") or payload.get("args") or payload.get("message", "")
+     if isinstance(content, dict):
+      content = json.dumps(content, indent=1)
+    with self._pending_history_adds_lock:
+     self._pending_history_adds.append({
+       "role": role,
+       "content": f"[{kind.upper().replace('_', ' ')}]\n{content}",
+       "collapsed": True,
+       "ts": entry.get("ts", project_manager.now_ts())
+      })
   if kind == "history_add":
    payload = entry.get("payload", {})
    with self._pending_history_adds_lock:
@@ -1973,7 +2004,6 @@ class AppController:
   self.ui_auto_scroll_comms = proj.get("project", {}).get("auto_scroll_comms", True)
   self.ui_auto_scroll_tool_calls = proj.get("project", {}).get("auto_scroll_tool_calls", True)
   self.ui_word_wrap = proj.get("project", {}).get("word_wrap", True)
-  self.ui_summary_only = proj.get("project", {}).get("summary_only", False)
   agent_tools_cfg = proj.get("agent", {}).get("tools", {})
   self.ui_agent_tools = {t: agent_tools_cfg.get(t, True) for t in models.AGENT_TOOL_NAMES}
   # MMA Tracks
@@ -2158,6 +2188,20 @@ class AppController:
   discussions[name] = project_manager.default_discussion()
   self._switch_discussion(name)
 
+ def _branch_discussion(self, index: int) -> None:
+  self._flush_disc_entries_to_project()
+  # Generate a unique branch name
+  base_name = self.active_discussion.split("_take_")[0]
+  counter = 1
+  new_name = f"{base_name}_take_{counter}"
+  disc_sec = self.project.get("discussion", {})
+  discussions = disc_sec.get("discussions", {})
+  while new_name in discussions:
+   counter += 1
+   new_name = f"{base_name}_take_{counter}"
+
+  project_manager.branch_discussion(self.project, self.active_discussion, new_name, index)
+  self._switch_discussion(new_name)
  def _rename_discussion(self, old_name: str, new_name: str) -> None:
   disc_sec = self.project.get("discussion", {})
   discussions = disc_sec.get("discussions", {})
@@ -2411,7 +2455,6 @@ class AppController:
   proj["project"]["main_context"] = self.ui_project_main_context
   proj["project"]["active_preset"] = self.ui_project_preset_name
   proj["project"]["word_wrap"] = self.ui_word_wrap
-  proj["project"]["summary_only"] = self.ui_summary_only
   proj["project"]["auto_scroll_comms"] = self.ui_auto_scroll_comms
   proj["project"]["auto_scroll_tool_calls"] = self.ui_auto_scroll_tool_calls
   proj.setdefault("gemini_cli", {})["binary_path"] = self.ui_gemini_cli_path
@@ -2485,6 +2528,11 @@ class AppController:
   # Build discussion history text separately
   history = flat.get("discussion", {}).get("history", [])
   discussion_text = aggregate.build_discussion_text(history)
+  
+  csp = filter(bool, [self.ui_global_system_prompt.strip(), self.ui_project_system_prompt.strip()])
+  self.last_resolved_system_prompt = "\n\n".join(csp)
+  self.last_aggregate_markdown = full_md
+  
   return full_md, path, file_items, stable_md, discussion_text
 
  def _cb_plan_epic(self) -> None:

src/events.py

@@ -91,7 +91,14 @@ class AsyncEventQueue:
   """
   self._queue.put((event_name, payload))
   if self.websocket_server:
-   self.websocket_server.broadcast("events", {"event": event_name, "payload": payload})
+   # Ensure payload is JSON serializable for websocket broadcast
+   serializable_payload = payload
+   if hasattr(payload, 'to_dict'):
+    serializable_payload = payload.to_dict()
+   elif hasattr(payload, '__dict__'):
+    serializable_payload = vars(payload)
+   
+   self.websocket_server.broadcast("events", {"event": event_name, "payload": serializable_payload})
 
  def get(self) -> Tuple[str, Any]:
   """

src/models.py

@@ -111,6 +111,7 @@ DEFAULT_TOOL_CATEGORIES: Dict[str, List[str]] = {
 
 def parse_history_entries(history_strings: list[str], roles: list[str]) -> list[dict[str, Any]]:
  import re
+ from src import thinking_parser
  entries = []
  for raw in history_strings:
   ts = ""
@@ -128,11 +129,30 @@ def parse_history_entries(history_strings: list[str], roles: list[str]) -> list[
    content = rest[match.end():].strip()
   else:
    content = rest
-  entries.append({"role": role, "content": content, "collapsed": True, "ts": ts})
+   
+  entry_obj = {"role": role, "content": content, "collapsed": True, "ts": ts}
+  if role == "AI" and ("<thinking>" in content or "<thought>" in content or "Thinking:" in content):
+   segments, parsed_content = thinking_parser.parse_thinking_trace(content)
+   if segments:
+    entry_obj["content"] = parsed_content
+    entry_obj["thinking_segments"] = [{"content": s.content, "marker": s.marker} for s in segments]
+    
+  entries.append(entry_obj)
  return entries
 
 @dataclass
-@dataclass
+class ThinkingSegment:
+ content: str
+ marker: str # 'thinking', 'thought', or 'Thinking:'
+
+ def to_dict(self) -> Dict[str, Any]:
+  return {"content": self.content, "marker": self.marker}
+
+ @classmethod
+ def from_dict(cls, data: Dict[str, Any]) -> "ThinkingSegment":
+  return cls(content=data["content"], marker=data["marker"])
+
+
 @dataclass
 class Ticket:
  id: str
@@ -239,8 +259,6 @@ class Track:
   )
 
 
-@dataclass
-@dataclass
 @dataclass
 class WorkerContext:
  ticket_id: str
@@ -339,12 +357,14 @@ class FileItem:
  path: str
  auto_aggregate: bool = True
  force_full: bool = False
+ injected_at: Optional[float] = None
 
  def to_dict(self) -> Dict[str, Any]:
   return {
    "path": self.path,
    "auto_aggregate": self.auto_aggregate,
    "force_full": self.force_full,
+   "injected_at": self.injected_at,
   }
 
  @classmethod
@@ -353,6 +373,7 @@ class FileItem:
    path=data["path"],
    auto_aggregate=data.get("auto_aggregate", True),
    force_full=data.get("force_full", False),
+   injected_at=data.get("injected_at"),
   )
 
 @dataclass
@@ -448,6 +469,7 @@ class Persona:
  system_prompt: str = ''
  tool_preset: Optional[str] = None
  bias_profile: Optional[str] = None
+ context_preset: Optional[str] = None
 
  @property
  def provider(self) -> Optional[str]:
@@ -490,6 +512,8 @@ class Persona:
    res["tool_preset"] = self.tool_preset
   if self.bias_profile is not None:
    res["bias_profile"] = self.bias_profile
+  if self.context_preset is not None:
+   res["context_preset"] = self.context_preset
   return res
 
  @classmethod
@@ -507,7 +531,7 @@ class Persona:
   for k in ["provider", "model", "temperature", "top_p", "max_output_tokens"]:
    if data.get(k) is not None:
     legacy[k] = data[k]
-  
+
   if legacy:
    if not parsed_models:
     parsed_models.append(legacy)
@@ -523,8 +547,8 @@ class Persona:
    system_prompt=data.get("system_prompt", ""),
    tool_preset=data.get("tool_preset"),
    bias_profile=data.get("bias_profile"),
+   context_preset=data.get("context_preset"),
   )
-
 @dataclass
 class MCPServerConfig:
  name: str

src/project_manager.py

@@ -33,6 +33,14 @@ def entry_to_str(entry: dict[str, Any]) -> str:
  ts = entry.get("ts", "")
  role = entry.get("role", "User")
  content = entry.get("content", "")
+ 
+ segments = entry.get("thinking_segments")
+ if segments:
+  for s in segments:
+   marker = s.get("marker", "thinking")
+   s_content = s.get("content", "")
+   content = f"<{marker}>\n{s_content}\n</{marker}>\n{content}"
+   
  if ts:
   return f"@{ts}\n{role}:\n{content}"
  return f"{role}:\n{content}"
@@ -93,6 +101,7 @@ def default_project(name: str = "unnamed") -> dict[str, Any]:
   "output":      {"output_dir": "./md_gen"},
   "files":       {"base_dir": ".", "paths": [], "tier_assignments": {}},
   "screenshots": {"base_dir": ".", "paths": []},
+  "context_presets": {},
   "gemini_cli":  {"binary_path": "gemini"},
   "deepseek":    {"reasoning_effort": "medium"},
   "agent":       {
@@ -231,15 +240,37 @@ def flat_config(proj: dict[str, Any], disc_name: Optional[str] = None, track_id:
   disc_data = disc_sec.get("discussions", {}).get(name, {})
   history = disc_data.get("history", [])
  return {
-  "project":     proj.get("project", {}),
-  "output":      proj.get("output", {}),
-  "files":       proj.get("files",  {}),
-  "screenshots": proj.get("screenshots", {}),
-  "discussion":  {
+  "project":         proj.get("project", {}),
+  "output":          proj.get("output", {}),
+  "files":           proj.get("files",  {}),
+  "screenshots":     proj.get("screenshots", {}),
+  "context_presets": proj.get("context_presets", {}),
+  "discussion":      {
    "roles":   disc_sec.get("roles", []),
    "history": history,
   },
  }
+ # ── context presets ──────────────────────────────────────────────────────────
+
+def save_context_preset(project_dict: dict, preset_name: str, files: list[str], screenshots: list[str]) -> None:
+ """Save a named context preset (files + screenshots) into the project dict."""
+ if "context_presets" not in project_dict:
+  project_dict["context_presets"] = {}
+ project_dict["context_presets"][preset_name] = {
+  "files": files,
+  "screenshots": screenshots
+ }
+
+def load_context_preset(project_dict: dict, preset_name: str) -> dict:
+ """Return the files and screenshots for a named preset."""
+ if "context_presets" not in project_dict or preset_name not in project_dict["context_presets"]:
+  raise KeyError(f"Preset '{preset_name}' not found in project context_presets.")
+ return project_dict["context_presets"][preset_name]
+
+def delete_context_preset(project_dict: dict, preset_name: str) -> None:
+ """Remove a named preset if it exists."""
+ if "context_presets" in project_dict:
+  project_dict["context_presets"].pop(preset_name, None)
  # ── track state persistence ─────────────────────────────────────────────────
 
 def save_track_state(track_id: str, state: 'TrackState', base_dir: Union[str, Path] = ".") -> None:
@@ -393,3 +424,36 @@ def calculate_track_progress(tickets: list) -> dict:
   "todo": todo
  }
 
+
+def branch_discussion(project_dict: dict, source_id: str, new_id: str, message_index: int) -> None:
+ """
+ Creates a new discussion in project_dict['discussion']['discussions'] by copying 
+ the history from source_id up to (and including) message_index, and sets active to new_id.
+ """
+ if "discussion" not in project_dict or "discussions" not in project_dict["discussion"]:
+  return
+ if source_id not in project_dict["discussion"]["discussions"]:
+  return
+ 
+ source_disc = project_dict["discussion"]["discussions"][source_id]
+ new_disc = default_discussion()
+ new_disc["git_commit"] = source_disc.get("git_commit", "")
+ # Copy history up to and including message_index
+ new_disc["history"] = source_disc["history"][:message_index + 1]
+ 
+ project_dict["discussion"]["discussions"][new_id] = new_disc
+ project_dict["discussion"]["active"] = new_id
+
+def promote_take(project_dict: dict, take_id: str, new_id: str) -> None:
+ """Renames a take_id to new_id in the discussions dict."""
+ if "discussion" not in project_dict or "discussions" not in project_dict["discussion"]:
+  return
+ if take_id not in project_dict["discussion"]["discussions"]:
+  return
+ 
+ disc = project_dict["discussion"]["discussions"].pop(take_id)
+ project_dict["discussion"]["discussions"][new_id] = disc
+ 
+ # If the take was active, update the active pointer
+ if project_dict["discussion"].get("active") == take_id:
+  project_dict["discussion"]["active"] = new_id

src/synthesis_formatter.py

@@ -0,0 +1,42 @@
+def format_takes_diff(takes: dict[str, list[dict]]) -> str:
+ if not takes:
+  return ""
+ 
+ histories = list(takes.values())
+ if not histories:
+  return ""
+
+ min_len = min(len(h) for h in histories)
+ common_prefix_len = 0
+ for i in range(min_len):
+  first_msg = histories[0][i]
+  if all(h[i] == first_msg for h in histories):
+   common_prefix_len += 1
+  else:
+   break
+
+ shared_lines = []
+ for i in range(common_prefix_len):
+  msg = histories[0][i]
+  shared_lines.append(f"{msg.get('role', 'unknown')}: {msg.get('content', '')}")
+ 
+ shared_text = "=== Shared History ==="
+ if shared_lines:
+  shared_text += "\n" + "\n".join(shared_lines)
+
+ variation_lines = []
+ if len(takes) > 1:
+  for take_name, history in takes.items():
+   if len(history) > common_prefix_len:
+    variation_lines.append(f"[{take_name}]")
+    for i in range(common_prefix_len, len(history)):
+     msg = history[i]
+     variation_lines.append(f"{msg.get('role', 'unknown')}: {msg.get('content', '')}")
+    variation_lines.append("")
+ else:
+  # Single take case
+  pass
+
+ variations_text = "=== Variations ===\n" + "\n".join(variation_lines)
+
+ return shared_text + "\n\n" + variations_text

src/thinking_parser.py

@@ -0,0 +1,53 @@
+import re
+from typing import List, Tuple
+from src.models import ThinkingSegment
+
+def parse_thinking_trace(text: str) -> Tuple[List[ThinkingSegment], str]:
+ """
+ Parses thinking segments from text and returns (segments, response_content).
+ Support extraction of thinking traces from <thinking>...</thinking>, <thought>...</thought>,
+ and blocks prefixed with Thinking:.
+ """
+ segments = []
+ 
+ # 1. Extract <thinking> and <thought> tags
+ current_text = text
+ 
+ # Combined pattern for tags
+ tag_pattern = re.compile(r'<(thinking|thought)>(.*?)</\1>', re.DOTALL | re.IGNORECASE)
+ 
+ def extract_tags(txt: str) -> Tuple[List[ThinkingSegment], str]:
+  found_segments = []
+  
+  def replace_func(match):
+   marker = match.group(1).lower()
+   content = match.group(2).strip()
+   found_segments.append(ThinkingSegment(content=content, marker=marker))
+   return ""
+  
+  remaining = tag_pattern.sub(replace_func, txt)
+  return found_segments, remaining
+
+ tag_segments, remaining = extract_tags(current_text)
+ segments.extend(tag_segments)
+ 
+ # 2. Extract Thinking: prefix
+ # This usually appears at the start of a block and ends with a double newline or a response marker.
+ thinking_colon_pattern = re.compile(r'(?:^|\n)Thinking:\s*(.*?)(?:\n\n|\nResponse:|\nAnswer:|$)', re.DOTALL | re.IGNORECASE)
+ 
+ def extract_colon_blocks(txt: str) -> Tuple[List[ThinkingSegment], str]:
+  found_segments = []
+  
+  def replace_func(match):
+   content = match.group(1).strip()
+   if content:
+    found_segments.append(ThinkingSegment(content=content, marker="Thinking:"))
+   return "\n\n"
+  
+  res = thinking_colon_pattern.sub(replace_func, txt)
+  return found_segments, res
+
+ colon_segments, final_remaining = extract_colon_blocks(remaining)
+ segments.extend(colon_segments)
+ 
+ return segments, final_remaining.strip()

tests/test_context_presets.py

@@ -0,0 +1,59 @@
+import pytest
+from src.project_manager import (
+ save_context_preset,
+ load_context_preset,
+ delete_context_preset
+)
+
+def test_save_context_preset():
+ project_dict = {}
+ preset_name = "test_preset"
+ files = ["file1.py", "file2.py"]
+ screenshots = ["screenshot1.png"]
+ 
+ save_context_preset(project_dict, preset_name, files, screenshots)
+ 
+ assert "context_presets" in project_dict
+ assert preset_name in project_dict["context_presets"]
+ assert project_dict["context_presets"][preset_name]["files"] == files
+ assert project_dict["context_presets"][preset_name]["screenshots"] == screenshots
+
+def test_load_context_preset():
+ project_dict = {
+  "context_presets": {
+   "test_preset": {
+    "files": ["file1.py"],
+    "screenshots": ["screenshot1.png"]
+   }
+  }
+ }
+ 
+ preset = load_context_preset(project_dict, "test_preset")
+ 
+ assert preset["files"] == ["file1.py"]
+ assert preset["screenshots"] == ["screenshot1.png"]
+
+def test_load_nonexistent_preset():
+ project_dict = {"context_presets": {}}
+ with pytest.raises(KeyError):
+  load_context_preset(project_dict, "nonexistent")
+
+def test_delete_context_preset():
+ project_dict = {
+  "context_presets": {
+   "test_preset": {
+    "files": ["file1.py"],
+    "screenshots": []
+   }
+  }
+ }
+ 
+ delete_context_preset(project_dict, "test_preset")
+ 
+ assert "test_preset" not in project_dict["context_presets"]
+
+def test_delete_nonexistent_preset_no_error():
+ project_dict = {"context_presets": {}}
+ # Should not raise error if it doesn't exist
+ delete_context_preset(project_dict, "nonexistent")
+ assert "nonexistent" not in project_dict["context_presets"]

tests/test_context_presets_removal.py

@@ -0,0 +1,14 @@
+import pytest
+import inspect
+
+
+def test_context_presets_tab_removed_from_project_settings():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._gui_func)
+    assert "Context Presets" not in source, (
+        "Context Presets tab should be removed from Project Settings"
+    )
+    assert "_render_context_presets_panel" not in source, (
+        "Context presets panel call should be removed"
+    )

tests/test_discussion_takes.py

@@ -0,0 +1,50 @@
+import unittest
+from src import project_manager
+
+class TestDiscussionTakes(unittest.TestCase):
+ def setUp(self):
+  self.project_dict = project_manager.default_project("test_branching")
+  # Populate initial history in 'main'
+  self.project_dict["discussion"]["discussions"]["main"]["history"] = [
+   "User: Message 0",
+   "AI: Response 0",
+   "User: Message 1",
+   "AI: Response 1",
+   "User: Message 2"
+  ]
+
+ def test_branch_discussion_creates_new_take(self):
+  """Verify that branch_discussion copies history up to index and sets active."""
+  source_id = "main"
+  new_id = "take_1"
+  message_index = 1
+  
+  # This will fail with AttributeError until implemented in project_manager.py
+  project_manager.branch_discussion(self.project_dict, source_id, new_id, message_index)
+  
+  # Asserts
+  self.assertIn(new_id, self.project_dict["discussion"]["discussions"])
+  new_history = self.project_dict["discussion"]["discussions"][new_id]["history"]
+  self.assertEqual(len(new_history), 2)
+  self.assertEqual(new_history[0], "User: Message 0")
+  self.assertEqual(new_history[1], "AI: Response 0")
+  self.assertEqual(self.project_dict["discussion"]["active"], new_id)
+
+ def test_promote_take_renames_discussion(self):
+  """Verify that promote_take renames a discussion key."""
+  take_id = "take_experimental"
+  self.project_dict["discussion"]["discussions"][take_id] = project_manager.default_discussion()
+  self.project_dict["discussion"]["discussions"][take_id]["history"] = ["User: Experimental"]
+  
+  new_id = "feature_refined"
+  
+  # This will fail with AttributeError until implemented in project_manager.py
+  project_manager.promote_take(self.project_dict, take_id, new_id)
+  
+  # Asserts
+  self.assertNotIn(take_id, self.project_dict["discussion"]["discussions"])
+  self.assertIn(new_id, self.project_dict["discussion"]["discussions"])
+  self.assertEqual(self.project_dict["discussion"]["discussions"][new_id]["history"], ["User: Experimental"])
+
+if __name__ == "__main__":
+ unittest.main()

tests/test_discussion_takes_gui.py

@@ -0,0 +1,96 @@
+import pytest
+from unittest.mock import MagicMock, patch, call
+from src.gui_2 import App
+
+@pytest.fixture
+def app_instance():
+ with (
+  patch('src.models.load_config', return_value={'ai': {'provider': 'gemini', 'model': 'gemini-2.5-flash-lite'}, 'projects': {}}),
+  patch('src.models.save_config'),
+  patch('src.gui_2.project_manager'),
+  patch('src.gui_2.session_logger'),
+  patch('src.gui_2.immapp.run'),
+  patch('src.app_controller.AppController._load_active_project'),
+  patch('src.app_controller.AppController._fetch_models'),
+  patch.object(App, '_load_fonts'),
+  patch.object(App, '_post_init'),
+  patch('src.app_controller.AppController._prune_old_logs'),
+  patch('src.app_controller.AppController.start_services'),
+  patch('src.api_hooks.HookServer'),
+  patch('src.ai_client.set_provider'),
+  patch('src.ai_client.reset_session')
+ ):
+  app = App()
+  # Setup project discussions
+  app.project = {
+   "discussion": {
+    "active": "main",
+    "discussions": {
+     "main": {"history": []},
+     "take_1": {"history": []},
+     "take_2": {"history": []}
+    }
+   }
+  }
+  app.active_discussion = "main"
+  app.is_viewing_prior_session = False
+  app.ui_disc_new_name_input = ""
+  app.ui_disc_truncate_pairs = 1
+  yield app
+
+def test_render_discussion_tabs(app_instance):
+ """Verify that _render_discussion_panel uses tabs for discussions."""
+ with patch('src.gui_2.imgui') as mock_imgui:
+  # Setup defaults for common imgui calls to avoid unpacking errors
+  mock_imgui.collapsing_header.return_value = True
+  mock_imgui.begin_combo.return_value = False
+  mock_imgui.input_text.return_value = (False, "")
+  mock_imgui.input_int.return_value = (False, 0)
+  mock_imgui.button.return_value = False
+  mock_imgui.checkbox.return_value = (False, False)
+  mock_imgui.begin_child.return_value = True
+  mock_imgui.selectable.return_value = (False, False)
+  
+  # Mock tab bar calls
+  mock_imgui.begin_tab_bar.return_value = True
+  mock_imgui.begin_tab_item.return_value = (False, False)
+
+  app_instance._render_discussion_panel()
+
+  # Check if begin_tab_bar was called
+  # This SHOULD fail if it's not implemented yet
+  mock_imgui.begin_tab_bar.assert_called_with("##discussion_tabs")
+  
+  # Check if begin_tab_item was called for each discussion
+  names = sorted(["main", "take_1", "take_2"])
+  for name in names:
+   mock_imgui.begin_tab_item.assert_any_call(name)
+
+def test_switching_discussion_via_tabs(app_instance):
+ """Verify that clicking a tab switches the discussion."""
+ with patch('src.gui_2.imgui') as mock_imgui, \
+      patch('src.app_controller.AppController._switch_discussion') as mock_switch:
+  # Setup defaults
+  mock_imgui.collapsing_header.return_value = True
+  mock_imgui.begin_combo.return_value = False
+  mock_imgui.input_text.return_value = (False, "")
+  mock_imgui.input_int.return_value = (False, 0)
+  mock_imgui.button.return_value = False
+  mock_imgui.checkbox.return_value = (False, False)
+  mock_imgui.begin_child.return_value = True
+  mock_imgui.selectable.return_value = (False, False)
+
+  mock_imgui.begin_tab_bar.return_value = True
+  
+  # Simulate 'take_1' being active/selected
+  def side_effect(name, flags=None):
+   if name == "take_1":
+    return (True, True)
+   return (False, True)
+  
+  mock_imgui.begin_tab_item.side_effect = side_effect
+  
+  app_instance._render_discussion_panel()
+  
+  # If implemented with tabs, this should be called
+  mock_switch.assert_called_with("take_1")

tests/test_file_item_model.py

@@ -7,6 +7,7 @@ def test_file_item_fields():
  assert item.path == "src/models.py"
  assert item.auto_aggregate is True
  assert item.force_full is False
+ assert item.injected_at is None
 
 def test_file_item_to_dict():
  """Test that FileItem can be serialized to a dict."""
@@ -14,7 +15,8 @@ def test_file_item_to_dict():
  expected = {
   "path": "test.py",
   "auto_aggregate": False,
-  "force_full": True
+  "force_full": True,
+  "injected_at": None
  }
  assert item.to_dict() == expected
 
@@ -23,12 +25,14 @@ def test_file_item_from_dict():
  data = {
   "path": "test.py",
   "auto_aggregate": False,
-  "force_full": True
+  "force_full": True,
+  "injected_at": 123.456
  }
  item = FileItem.from_dict(data)
  assert item.path == "test.py"
  assert item.auto_aggregate is False
  assert item.force_full is True
+ assert item.injected_at == 123.456
 
 def test_file_item_from_dict_defaults():
  """Test that FileItem.from_dict handles missing fields."""
@@ -37,3 +41,4 @@ def test_file_item_from_dict_defaults():
  assert item.path == "test.py"
  assert item.auto_aggregate is True
  assert item.force_full is False
+ assert item.injected_at is None

tests/test_gui2_layout.py

@@ -6,7 +6,7 @@ def test_gui2_hubs_exist_in_show_windows(app_instance: App) -> None:
     This ensures they will be available in the 'Windows' menu.
     """
  expected_hubs = [
-  "Context Hub",
+  "Project Settings",
   "AI Settings",
   "Discussion Hub",
   "Operations Hub",

tests/test_gui_context_presets.py

@@ -0,0 +1,35 @@
+import pytest
+import time
+from src.api_hook_client import ApiHookClient
+
+def test_gui_context_preset_save_load(live_gui) -> None:
+ """Verify that saving and loading context presets works via the GUI app."""
+ client = ApiHookClient()
+ assert client.wait_for_server(timeout=15)
+
+ preset_name = "test_gui_preset"
+ test_files = ["test.py"]
+ test_screenshots = ["test.png"]
+
+ client.push_event("custom_callback", {"callback": "simulate_save_preset", "args": [preset_name]})
+ time.sleep(1.5)
+
+ project_data = client.get_project()
+ project = project_data.get("project", {})
+ presets = project.get("context_presets", {})
+ 
+ assert preset_name in presets, f"Preset '{preset_name}' not found in project context_presets"
+ 
+ preset_entry = presets[preset_name]
+ preset_files = [f["path"] if isinstance(f, dict) else str(f) for f in preset_entry.get("files", [])]
+ assert preset_files == test_files
+ assert preset_entry.get("screenshots", []) == test_screenshots
+
+ # Load the preset
+ client.push_event("custom_callback", {"callback": "load_context_preset", "args": [preset_name]})
+ time.sleep(1.0)
+
+ context = client.get_context_state()
+ loaded_files = [f["path"] if isinstance(f, dict) else str(f) for f in context.get("files", [])]
+ assert loaded_files == test_files
+ assert context.get("screenshots", []) == test_screenshots

tests/test_gui_discussion_tabs.py

@@ -0,0 +1,53 @@
+import pytest
+from unittest.mock import patch, MagicMock, PropertyMock
+
+from src import gui_2
+
+@pytest.fixture
+def mock_gui():
+    gui = gui_2.App()
+    gui.project = {
+        'discussion': {
+            'active': 'main',
+            'discussions': {
+                'main': {'history': []},
+                'main_take_1': {'history': []},
+                'other_topic': {'history': []}
+            }
+        }
+    }
+    gui.active_discussion = 'main'
+    gui.perf_profiling_enabled = False
+    gui.is_viewing_prior_session = False
+    gui._get_discussion_names = lambda: ['main', 'main_take_1', 'other_topic']
+    return gui
+
+def test_discussion_tabs_rendered(mock_gui):
+    with patch('src.gui_2.imgui') as mock_imgui, \
+         patch('src.app_controller.AppController.active_project_root', new_callable=PropertyMock, return_value='.'):
+        
+        # We expect a combo box for base discussion
+        mock_imgui.begin_combo.return_value = True
+        mock_imgui.selectable.return_value = (False, False)
+        
+        # We expect a tab bar for takes
+        mock_imgui.begin_tab_bar.return_value = True
+        mock_imgui.begin_tab_item.return_value = (True, True)
+        mock_imgui.input_text.return_value = (False, "")
+        mock_imgui.input_text_multiline.return_value = (False, "")
+        mock_imgui.checkbox.return_value = (False, False)
+        mock_imgui.input_int.return_value = (False, 0)
+        
+        mock_clipper = MagicMock()
+        mock_clipper.step.return_value = False
+        mock_imgui.ListClipper.return_value = mock_clipper
+        
+        mock_gui._render_discussion_panel()
+        
+        mock_imgui.begin_combo.assert_called_once_with("##disc_sel", 'main')
+        mock_imgui.begin_tab_bar.assert_called_once_with('discussion_takes_tabs')
+        
+        calls = [c[0][0] for c in mock_imgui.begin_tab_item.call_args_list]
+        assert 'Original###main' in calls
+        assert 'Take 1###main_take_1' in calls
+        assert 'Synthesis###Synthesis' in calls

tests/test_gui_phase4.py

@@ -91,6 +91,7 @@ def test_track_discussion_toggle(mock_app: App):
   mock_imgui.button.return_value = False
   mock_imgui.collapsing_header.return_value = True # For Discussions header
   mock_imgui.input_text.side_effect = lambda label, value, *args, **kwargs: (False, value)
+  mock_imgui.input_text_multiline.side_effect = lambda label, value, *args, **kwargs: (False, value)
   mock_imgui.input_int.side_effect = lambda label, value, *args, **kwargs: (False, value)
   mock_imgui.begin_child.return_value = True
   # Mock clipper to avoid the while loop hang

tests/test_gui_symbol_navigation.py

@@ -8,7 +8,8 @@ def test_render_discussion_panel_symbol_lookup(mock_app, role):
  with (
   patch('src.gui_2.imgui') as mock_imgui,
   patch('src.gui_2.mcp_client') as mock_mcp,
-  patch('src.gui_2.project_manager') as mock_pm
+  patch('src.gui_2.project_manager') as mock_pm,
+  patch('src.markdown_helper.imgui_md') as mock_md
  ):
   # Set up App instance state
   mock_app.perf_profiling_enabled = False

tests/test_gui_synthesis.py

@@ -0,0 +1,56 @@
+import pytest
+from unittest.mock import MagicMock, patch, ANY
+from src.gui_2 import App
+
+@pytest.fixture
+def app_instance():
+ with (
+  patch('src.models.load_config', return_value={'ai': {'provider': 'gemini', 'model': 'gemini-2.5-flash-lite'}, 'projects': {}}),
+  patch('src.models.save_config'),
+  patch('src.gui_2.project_manager'),
+  patch('src.gui_2.session_logger'),
+  patch('src.gui_2.immapp.run'),
+  patch('src.app_controller.AppController._load_active_project'),
+  patch('src.app_controller.AppController._fetch_models'),
+  patch.object(App, '_load_fonts'),
+  patch.object(App, '_post_init'),
+  patch('src.app_controller.AppController._prune_old_logs'),
+  patch('src.app_controller.AppController.start_services'),
+  patch('src.api_hooks.HookServer'),
+  patch('src.ai_client.set_provider'),
+  patch('src.ai_client.reset_session')
+ ):
+  app = App()
+  app.project = {
+   "discussion": {
+    "active": "main",
+    "discussions": {
+     "main": {"history": []},
+     "take_1": {"history": []},
+     "take_2": {"history": []}
+    }
+   }
+  }
+  app.ui_synthesis_prompt = "Summarize these takes"
+  yield app
+
+def test_render_synthesis_panel(app_instance):
+ """Verify that _render_synthesis_panel renders checkboxes for takes and input for prompt."""
+ with patch('src.gui_2.imgui') as mock_imgui:
+  mock_imgui.checkbox.return_value = (False, False)
+  mock_imgui.input_text_multiline.return_value = (False, app_instance.ui_synthesis_prompt)
+  mock_imgui.button.return_value = False
+
+  # Call the method we are testing
+  app_instance._render_synthesis_panel()
+
+  # 1. Assert imgui.checkbox is called for each take in project_dict['discussion']['discussions']
+  discussions = app_instance.project['discussion']['discussions']
+  for name in discussions:
+   mock_imgui.checkbox.assert_any_call(name, ANY)
+
+  # 2. Assert imgui.input_text_multiline is called for the prompt
+  mock_imgui.input_text_multiline.assert_called_with("##synthesis_prompt", app_instance.ui_synthesis_prompt, ANY)
+
+  # 3. Assert imgui.button is called for 'Generate Synthesis'
+  mock_imgui.button.assert_any_call("Generate Synthesis")

tests/test_gui_text_viewer.py

@@ -0,0 +1,28 @@
+import pytest
+import time
+from src.api_hook_client import ApiHookClient
+
+def test_text_viewer_state_update(live_gui) -> None:
+ """
+ Verifies that we can set text viewer state and it is reflected in GUI state.
+ """
+ client = ApiHookClient()
+ label = "Test Viewer Label"
+ content = "This is test content for the viewer."
+ text_type = "markdown"
+
+ # Add a task to push a custom callback that mutates the app state
+ def set_viewer_state(app):
+  app.show_text_viewer = True
+  app.text_viewer_title = label
+  app.text_viewer_content = content
+  app.text_viewer_type = text_type
+
+ client.push_event("custom_callback", {"callback": set_viewer_state})
+ time.sleep(0.5)
+ 
+ state = client.get_gui_state()
+ assert state is not None
+ assert state.get('show_text_viewer') == True
+ assert state.get('text_viewer_title') == label
+ assert state.get('text_viewer_type') == text_type

tests/test_layout_reorganization.py

@@ -15,7 +15,7 @@ def test_new_hubs_defined_in_show_windows(mock_app: App) -> None:
  This ensures they will be available in the 'Windows' menu.
  """
  expected_hubs = [
-  "Context Hub",
+  "Project Settings",
   "AI Settings",
   "Discussion Hub",
   "Operations Hub",
@@ -53,7 +53,7 @@ def test_hub_windows_exist_in_gui2(app_instance_simple: Any) -> None:
  """
  Verifies that the new Hub windows are present in the show_windows dictionary.
  """
- hubs = ["Context Hub", "AI Settings", "Discussion Hub", "Operations Hub"]
+ hubs = ["Project Settings", "AI Settings", "Discussion Hub", "Operations Hub"]
  for hub in hubs:
   assert hub in app_instance_simple.show_windows
 

tests/test_mma_approval_indicators.py

@@ -5,7 +5,7 @@ from src.gui_2 import App
 
 
 def _make_app(**kwargs):
- app = MagicMock(spec=App)
+ app = MagicMock()
  app.mma_streams = kwargs.get("mma_streams", {})
  app.mma_tier_usage = kwargs.get("mma_tier_usage", {
   "Tier 1": {"input": 0, "output": 0, "model": "gemini-3.1-pro-preview"},
@@ -13,6 +13,7 @@ def _make_app(**kwargs):
   "Tier 3": {"input": 0, "output": 0, "model": "gemini-2.5-flash-lite"},
   "Tier 4": {"input": 0, "output": 0, "model": "gemini-2.5-flash-lite"},
  })
+ app.ui_focus_agent = kwargs.get("ui_focus_agent", None)
  app.tracks = kwargs.get("tracks", [])
  app.active_track = kwargs.get("active_track", None)
  app.active_tickets = kwargs.get("active_tickets", [])

tests/test_project_settings_rename.py

@@ -0,0 +1,22 @@
+import pytest
+import inspect
+
+
+def test_context_hub_renamed_to_project_settings():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._gui_func)
+    assert "Project Settings" in source, (
+        "Context Hub should be renamed to Project Settings"
+    )
+    assert '"Context Hub"' not in source, '"Context Hub" string should be removed'
+
+
+def test_show_windows_key_updated():
+    import src.app_controller as app_controller
+
+    source = inspect.getsource(app_controller.AppController)
+    assert '"Project Settings"' in source or "'Project Settings'" in source, (
+        "show_windows key should be Project Settings"
+    )
+    assert '"Context Hub"' not in source, '"Context Hub" key should be removed'

tests/test_session_hub_merge.py

@@ -0,0 +1,42 @@
+import pytest
+import inspect
+
+
+def test_session_hub_window_removed():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._gui_func)
+    assert "Session Hub" not in source, "Session Hub window should be removed"
+
+
+def test_discussion_hub_has_snapshot_tab():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._gui_func)
+    assert "Snapshot" in source, "Discussion Hub should have Snapshot tab"
+    assert "_render_snapshot_tab" in source, "Discussion Hub should call _render_snapshot_tab"
+
+
+def test_discussion_hub_has_context_composition_placeholder():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._gui_func)
+    assert "Context Composition" in source, (
+        "Discussion Hub should have Context Composition tab placeholder"
+    )
+
+
+def test_discussion_hub_has_takes_tab():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._gui_func)
+    assert "Takes" in source, "Discussion Hub should have Takes tab"
+
+
+def test_show_windows_no_session_hub():
+    import src.app_controller as app_controller
+
+    source = inspect.getsource(app_controller.AppController)
+    assert "Session Hub" not in source, (
+        "Session Hub should be removed from show_windows"
+    )

tests/test_synthesis_formatter.py

@@ -0,0 +1,59 @@
+import pytest
+from src.synthesis_formatter import format_takes_diff
+
+def test_format_takes_diff_empty():
+ assert format_takes_diff({}) == ""
+
+def test_format_takes_diff_single_take():
+ takes = {
+  "take1": [
+   {"role": "user", "content": "hello"},
+   {"role": "assistant", "content": "hi"}
+  ]
+ }
+ expected = "=== Shared History ===\nuser: hello\nassistant: hi\n\n=== Variations ===\n"
+ assert format_takes_diff(takes) == expected
+
+def test_format_takes_diff_common_prefix():
+ takes = {
+  "take1": [
+   {"role": "user", "content": "hello"},
+   {"role": "assistant", "content": "hi"},
+   {"role": "user", "content": "how are you?"},
+   {"role": "assistant", "content": "I am fine."}
+  ],
+  "take2": [
+   {"role": "user", "content": "hello"},
+   {"role": "assistant", "content": "hi"},
+   {"role": "user", "content": "what is the time?"},
+   {"role": "assistant", "content": "It is noon."}
+  ]
+ }
+ expected = (
+  "=== Shared History ===\n"
+  "user: hello\n"
+  "assistant: hi\n\n"
+  "=== Variations ===\n"
+  "[take1]\n"
+  "user: how are you?\n"
+  "assistant: I am fine.\n\n"
+  "[take2]\n"
+  "user: what is the time?\n"
+  "assistant: It is noon.\n"
+ )
+ assert format_takes_diff(takes) == expected
+
+def test_format_takes_diff_no_common_prefix():
+ takes = {
+  "take1": [{"role": "user", "content": "a"}],
+  "take2": [{"role": "user", "content": "b"}]
+ }
+ expected = (
+  "=== Shared History ===\n\n"
+  "=== Variations ===\n"
+  "[take1]\n"
+  "user: a\n\n"
+  "[take2]\n"
+  "user: b\n"
+ )
+ assert format_takes_diff(takes) == expected

tests/test_thinking_gui.py

@@ -0,0 +1,53 @@
+import pytest
+
+
+def test_render_thinking_trace_helper_exists():
+    from src.gui_2 import App
+
+    assert hasattr(App, "_render_thinking_trace"), (
+        "_render_thinking_trace helper should exist in App class"
+    )
+
+
+def test_discussion_entry_with_thinking_segments():
+    entry = {
+        "role": "AI",
+        "content": "Here's my response",
+        "thinking_segments": [
+            {"content": "Let me analyze this step by step...", "marker": "thinking"},
+            {"content": "I should consider edge cases...", "marker": "thought"},
+        ],
+        "ts": "2026-03-13T10:00:00",
+        "collapsed": False,
+    }
+    assert "thinking_segments" in entry
+    assert len(entry["thinking_segments"]) == 2
+
+
+def test_discussion_entry_without_thinking():
+    entry = {
+        "role": "User",
+        "content": "Hello",
+        "ts": "2026-03-13T10:00:00",
+        "collapsed": False,
+    }
+    assert "thinking_segments" not in entry
+
+
+def test_thinking_segment_model_compatibility():
+    from src.models import ThinkingSegment
+
+    segment = ThinkingSegment(content="test", marker="thinking")
+    assert segment.content == "test"
+    assert segment.marker == "thinking"
+    d = segment.to_dict()
+    assert d["content"] == "test"
+    assert d["marker"] == "thinking"
+
+
+if __name__ == "__main__":
+    test_render_thinking_trace_helper_exists()
+    test_discussion_entry_with_thinking_segments()
+    test_discussion_entry_without_thinking()
+    test_thinking_segment_model_compatibility()
+    print("All GUI thinking trace tests passed!")

tests/test_thinking_persistence.py

@@ -0,0 +1,94 @@
+import pytest
+import tempfile
+import os
+from pathlib import Path
+from src import project_manager
+from src.models import ThinkingSegment
+
+
+def test_save_and_load_history_with_thinking_segments():
+    with tempfile.TemporaryDirectory() as tmpdir:
+        project_path = Path(tmpdir) / "test_project"
+        project_path.mkdir()
+
+        project_file = project_path / "test_project.toml"
+        project_file.write_text("[project]\nname = 'test'\n")
+
+        history_data = {
+            "entries": [
+                {
+                    "role": "AI",
+                    "content": "Here's the response",
+                    "thinking_segments": [
+                        {"content": "Let me think about this...", "marker": "thinking"}
+                    ],
+                    "ts": "2026-03-13T10:00:00",
+                    "collapsed": False,
+                },
+                {
+                    "role": "User",
+                    "content": "Hello",
+                    "ts": "2026-03-13T09:00:00",
+                    "collapsed": False,
+                },
+            ]
+        }
+
+        project_manager.save_project(
+            {"project": {"name": "test"}}, project_file, disc_data=history_data
+        )
+
+        loaded = project_manager.load_history(project_file)
+
+        assert "entries" in loaded
+        assert len(loaded["entries"]) == 2
+
+        ai_entry = loaded["entries"][0]
+        assert ai_entry["role"] == "AI"
+        assert ai_entry["content"] == "Here's the response"
+        assert "thinking_segments" in ai_entry
+        assert len(ai_entry["thinking_segments"]) == 1
+        assert (
+            ai_entry["thinking_segments"][0]["content"] == "Let me think about this..."
+        )
+
+        user_entry = loaded["entries"][1]
+        assert user_entry["role"] == "User"
+        assert "thinking_segments" not in user_entry
+
+
+def test_entry_to_str_with_thinking():
+    entry = {
+        "role": "AI",
+        "content": "Response text",
+        "thinking_segments": [{"content": "Thinking...", "marker": "thinking"}],
+        "ts": "2026-03-13T10:00:00",
+    }
+    result = project_manager.entry_to_str(entry)
+    assert "@2026-03-13T10:00:00" in result
+    assert "AI:" in result
+    assert "Response text" in result
+
+
+def test_str_to_entry_with_thinking():
+    raw = "@2026-03-13T10:00:00\nAI:\nResponse text"
+    roles = ["User", "AI", "Vendor API", "System", "Reasoning"]
+    result = project_manager.str_to_entry(raw, roles)
+    assert result["role"] == "AI"
+    assert result["content"] == "Response text"
+    assert "ts" in result
+
+
+def test_clean_nones_removes_thinking():
+    entry = {"role": "AI", "content": "Test", "thinking_segments": None, "ts": None}
+    cleaned = project_manager.clean_nones(entry)
+    assert "thinking_segments" not in cleaned
+    assert "ts" not in cleaned
+
+
+if __name__ == "__main__":
+    test_save_and_load_history_with_thinking_segments()
+    test_entry_to_str_with_thinking()
+    test_str_to_entry_with_thinking()
+    test_clean_nones_removes_thinking()
+    print("All project_manager thinking tests passed!")

tests/test_thinking_trace.py

@@ -0,0 +1,68 @@
+from src.thinking_parser import parse_thinking_trace
+
+
+def test_parse_xml_thinking_tag():
+    raw = "<thinking>\nLet me analyze this problem step by step.\n</thinking>\nHere is the answer."
+    segments, response = parse_thinking_trace(raw)
+    assert len(segments) == 1
+    assert segments[0].content == "Let me analyze this problem step by step."
+    assert segments[0].marker == "thinking"
+    assert response == "Here is the answer."
+
+
+def test_parse_xml_thought_tag():
+    raw = "<thought>This is my reasoning process</thought>\nFinal response here."
+    segments, response = parse_thinking_trace(raw)
+    assert len(segments) == 1
+    assert segments[0].content == "This is my reasoning process"
+    assert segments[0].marker == "thought"
+    assert response == "Final response here."
+
+
+def test_parse_text_thinking_prefix():
+    raw = "Thinking:\nThis is a text-based thinking trace.\n\nNow for the actual response."
+    segments, response = parse_thinking_trace(raw)
+    assert len(segments) == 1
+    assert segments[0].content == "This is a text-based thinking trace."
+    assert segments[0].marker == "Thinking:"
+    assert response == "Now for the actual response."
+
+
+def test_parse_no_thinking():
+    raw = "This is a normal response without any thinking markers."
+    segments, response = parse_thinking_trace(raw)
+    assert len(segments) == 0
+    assert response == raw
+
+
+def test_parse_empty_response():
+    segments, response = parse_thinking_trace("")
+    assert len(segments) == 0
+    assert response == ""
+
+
+def test_parse_multiple_markers():
+    raw = "<thinking>First thinking</thinking>\n<thought>Second thought</thought>\nResponse"
+    segments, response = parse_thinking_trace(raw)
+    assert len(segments) == 2
+    assert segments[0].content == "First thinking"
+    assert segments[1].content == "Second thought"
+
+
+def test_parse_thinking_with_empty_response():
+    raw = "<thinking>Just thinking, no response</thinking>"
+    segments, response = parse_thinking_trace(raw)
+    assert len(segments) == 1
+    assert segments[0].content == "Just thinking, no response"
+    assert response == ""
+
+
+if __name__ == "__main__":
+    test_parse_xml_thinking_tag()
+    test_parse_xml_thought_tag()
+    test_parse_text_thinking_prefix()
+    test_parse_no_thinking()
+    test_parse_empty_response()
+    test_parse_multiple_markers()
+    test_parse_thinking_with_empty_response()
+    print("All thinking trace tests passed!")

tests/test_ui_summary_only_removal.py

@@ -0,0 +1,75 @@
+import pytest
+import inspect
+from src import models
+
+
+def test_ui_summary_only_not_in_projects_panel():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._render_projects_panel)
+    assert "ui_summary_only" not in source, (
+        "ui_summary_only checkbox should be removed from Projects panel"
+    )
+    assert "Summary Only" not in source, (
+        "Summary Only label should be removed from Projects panel"
+    )
+
+
+def test_ui_summary_only_not_in_app_controller_projects():
+    import src.app_controller as app_controller
+
+    source = inspect.getsource(app_controller.AppController)
+    assert "ui_summary_only" not in source, (
+        "ui_summary_only should be removed from AppController"
+    )
+
+
+def test_file_item_has_per_file_flags():
+    item = models.FileItem(path="test.py")
+    assert hasattr(item, "auto_aggregate")
+    assert hasattr(item, "force_full")
+    assert item.auto_aggregate is True
+    assert item.force_full is False
+
+
+def test_file_item_serialization_with_flags():
+    item = models.FileItem(path="test.py", auto_aggregate=False, force_full=True)
+    data = item.to_dict()
+
+    assert data["auto_aggregate"] is False
+    assert data["force_full"] is True
+
+    restored = models.FileItem.from_dict(data)
+    assert restored.auto_aggregate is False
+    assert restored.force_full is True
+
+
+def test_project_without_summary_only_loads():
+    proj = {"project": {"name": "test", "paths": []}}
+    assert proj.get("project", {}).get("summary_only") is None
+
+
+def test_aggregate_from_items_respects_auto_aggregate():
+    from pathlib import Path
+    from src import aggregate
+
+    items = [
+        {
+            "path": Path("file1.py"),
+            "entry": "file1.py",
+            "content": "print('hello')",
+            "auto_aggregate": True,
+            "force_full": False,
+        },
+        {
+            "path": Path("file2.py"),
+            "entry": "file2.py",
+            "content": "print('world')",
+            "auto_aggregate": False,
+            "force_full": False,
+        },
+    ]
+
+    result = aggregate._build_files_section_from_items(items)
+    assert "file1.py" in result
+    assert "file2.py" not in result