conductor(plan): Phase 4 checkpoint complete

Takes panel implemented:
- List of takes with entry count
- Switch/delete actions per take
- Synthesis UI with take selection
- Uses existing synthesis_formatter

.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

.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
 ---
 

.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** � 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** � Previous tracks failed because specs
 asked to implement features that already existed.
 
 ### 2. Identify Gaps, Not Features

.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** � 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 � 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** � 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** � this is the Green phase
 
 ### 4. Refactor Phase (Optional)
 

.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

.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

check_hello_imgui.py

@@ -0,0 +1,9 @@
+
+import sys
+import os
+try:
+ from imgui_bundle import hello_imgui
+ rp = hello_imgui.RunnerParams()
+ print(f"Default borderless: {rp.app_window_params.borderless}")
+except Exception as e:
+ print(f"Error: {e}")

conductor/archive/external_mcp_support_20260308/plan.md

@@ -0,0 +1,42 @@
+# Implementation Plan: External MCP Server Support
+
+## Phase 1: Configuration & Data Modeling [checkpoint: 4ba1bd9]
+- [x] Task: Define the schema for external MCP server configuration. [1c863f0]
+    - [x] Update `src/models.py` to include `MCPServerConfig` and `MCPConfiguration` classes.
+    - [x] Implement logic to load `mcp_config.json` from global and project-specific paths.
+- [x] Task: Integrate configuration loading into `AppController`. [c09e0f5]
+    - [x] Ensure the MCP config path is correctly resolved from `config.toml` and `manual_slop.toml`.
+- [x] Task: Write unit tests for configuration loading and validation. [c09e0f5]
+- [x] Task: Conductor - User Manual Verification 'Phase 1: Configuration & Data Modeling' [4ba1bd9]
+
+## Phase 2: MCP Client Extension [checkpoint: 828fadf]
+- [x] Task: Implement `ExternalMCPManager` in `src/mcp_client.py`. [828fadf]
+    - [x] Add support for managing multiple MCP server sessions.
+    - [x] Implement the `StdioMCPClient` for local subprocess communication.
+    - [x] Implement the `RemoteMCPClient` for SSE/WebSocket communication (stub).
+- [x] Task: Update Tool Discovery. [828fadf]
+    - [x] Implement `list_external_tools()` to aggregate tools from all active external servers.
+- [x] Task: Update Tool Dispatch. [828fadf]
+    - [x] Modify `mcp_client.dispatch()` and `mcp_client.async_dispatch()` to route tool calls to either native tools or the appropriate external server.
+- [x] Task: Write integration tests for stdio and remote MCP client communication (using mock servers). [828fadf]
+- [x] Task: Conductor - User Manual Verification 'Phase 2: MCP Client Extension' [828fadf]
+
+## Phase 3: GUI Integration & Lifecycle [checkpoint: 3b2588a]
+- [x] Task: Update the **Operations** panel in `src/gui_2.py`. [3b2588a]
+    - [x] Create a new "External Tools" section.
+    - [x] List discovered tools from active external servers.
+    - [x] Add a "Refresh External MCPs" button to reload configuration and rediscover tools.
+- [x] Task: Implement Lifecycle Management. [3b2588a]
+    - [x] Add the "Auto-start on Project Load" logic to start servers when a project is initialized.
+    - [x] Add status indicators (e.g., color-coded dots) for each external server in the GUI.
+- [x] Task: Write visual regression tests or simulation scripts to verify the updated Operations panel. [3b2588a]
+- [x] Task: Conductor - User Manual Verification 'Phase 3: GUI Integration & Lifecycle' [3b2588a]
+
+## Phase 4: Agent Integration & HITL [checkpoint: f4c5a0b]
+- [x] Task: Update AI tool declarations. [f4c5a0b]
+    - [x] Ensure `ai_client.py` includes external tools in the tool definitions sent to Gemini/Anthropic.
+- [x] Task: Verify HITL Approval Flow. [f4c5a0b]
+    - [x] Ensure that calling an external tool correctly triggers the `ConfirmDialog` modal.
+    - [x] Verify that approved external tool results are correctly returned to the AI.
+- [x] Task: Perform a final end-to-end verification with a real external MCP server. [f4c5a0b]
+- [x] Task: Conductor - User Manual Verification 'Phase 4: Agent Integration & HITL' [f4c5a0b]

conductor/archive/frosted_glass_20260313/index.md

@@ -0,0 +1,5 @@
+# Track frosted_glass_20260313 Context
+
+- [Specification](./spec.md)
+- [Implementation Plan](./plan.md)
+- [Metadata](./metadata.json)

conductor/archive/frosted_glass_20260313/metadata.json

@@ -0,0 +1,8 @@
+{
+  "track_id": "frosted_glass_20260313",
+  "type": "feature",
+  "status": "new",
+  "created_at": "2026-03-13T14:39:00Z",
+  "updated_at": "2026-03-13T14:39:00Z",
+  "description": "Add 'frosted glass' bg for transparency on panels and popups. This blurring effect will allow drop downs and other elements of these panels to not get hard to discern from background text or elements behind the panel."
+}

conductor/archive/frosted_glass_20260313/plan.md

@@ -0,0 +1,26 @@
+# Implementation Plan: Frosted Glass Background Effect
+
+## Phase 1: Shader Development & Integration
+- [ ] Task: Audit `src/shader_manager.py` to identify existing background/post-process integration points.
+- [ ] Task: Write Tests: Verify `ShaderManager` can compile and bind a multi-pass blur shader.
+- [ ] Task: Implement: Add `FrostedGlassShader` (GLSL) to `src/shader_manager.py`.
+- [ ] Task: Implement: Integrate the blur shader into the `ShaderManager` lifecycle.
+- [ ] Task: Conductor - User Manual Verification 'Phase 1: Shader Development & Integration' (Protocol in workflow.md)
+
+## Phase 2: Framebuffer Capture Pipeline
+- [ ] Task: Write Tests: Verify the FBO capture mechanism correctly samples the back buffer and stores it in a texture.
+- [ ] Task: Implement: Update `src/shader_manager.py` or `src/gui_2.py` to handle "pre-rendering" of the background into a texture for blurring.
+- [ ] Task: Implement: Ensure the blurred texture is updated every frame or on window move events.
+- [ ] Task: Conductor - User Manual Verification 'Phase 2: Framebuffer Capture Pipeline' (Protocol in workflow.md)
+
+## Phase 3: GUI Integration & Rendering
+- [ ] Task: Write Tests: Verify that a mocked ImGui window successfully calls the frosted glass rendering logic.
+- [ ] Task: Implement: Create a `_render_frosted_background(self, pos, size)` helper in `src/gui_2.py`.
+- [ ] Task: Implement: Update panel rendering loops (e.g. `_gui_func`) to inject the frosted background before calling `imgui.begin()` for major panels.
+- [ ] Task: Conductor - User Manual Verification 'Phase 3: GUI Integration & Rendering' (Protocol in workflow.md)
+
+## Phase 4: UI Controls & Configuration
+- [ ] Task: Write Tests: Verify that modifying blur uniforms via the Live Editor updates the shader state.
+- [ ] Task: Implement: Add "Frosted Glass" sliders (Blur, Tint, Opacity) to the **Shader Editor** in `src/gui_2.py`.
+- [ ] Task: Implement: Update `src/theme.py` to parse and store frosted glass settings from `config.toml`.
+- [ ] Task: Conductor - User Manual Verification 'Phase 4: UI Controls & Configuration' (Protocol in workflow.md)

conductor/archive/frosted_glass_20260313/spec.md

@@ -0,0 +1,34 @@
+# Specification: Frosted Glass Background Effect
+
+## Overview
+Implement a high-fidelity "frosted glass" (acrylic) background effect for all GUI panels and popups within the Manual Slop interface. This effect will use a GPU-resident shader to blur the content behind active windows, improving readability and visual depth while preventing background text from clashing with foreground UI elements.
+
+## Functional Requirements
+- **GPU-Accelerated Blur:**
+  - Implement a GLSL fragment shader (e.g., Gaussian or Kawase blur) within the existing `ShaderManager` pipeline.
+  - The shader must sample the current frame buffer background and render a blurred version behind the active window's background.
+- **Global Integration:**
+  - The effect must automatically apply to all standard ImGui panels and popups.
+  - Integrate with `imgui.begin()` and `imgui.begin_popup()` (or via a reusable wrapper helper).
+- **Real-Time Tuning:**
+  - Add controls to the **Live Shader Editor** to adjust the following parameters:
+    - **Blur Radius:** Control the intensity of the Gaussian blur.
+    - **Tint Intensity:** Control the strength of the "frost" overlay color.
+    - **Base Opacity:** Control the overall transparency of the frosted layer.
+- **Persistence:**
+  - Save frosted glass parameters to `config.toml` under the `theme` or `shader` section.
+
+## Technical Implementation
+- **Shader Pipeline:** Use `PyOpenGL` to manage a dedicated background texture/FBO for sampling.
+- **Coordinate Mapping:** Ensure the blur shader correctly maps screen coordinates to the region behind the current ImGui window.
+- **State Integration:** Store tuning parameters in `App.shader_uniforms` and ensure they are updated every frame.
+
+## Acceptance Criteria
+- [ ] Panels and popups have a distinct, blurred background that clearly separates them from the content behind them.
+- [ ] Changing the "Blur Radius" slider in the Shader Editor immediately updates the visual frostiness.
+- [ ] The effect remains stable during window dragging and resizing.
+- [ ] No significant performance degradation (maintaining target FPS).
+
+## Out of Scope
+- Implementing different blur types (e.g., motion blur, radial blur).
+- Per-panel unique blur settings (initially global only).

conductor/archive/gui_path_config_20260308/plan.md

@@ -3,13 +3,13 @@
 ## Phase 1: Path Info Display
 Focus: Show current path resolution in GUI
 
-- [ ] Task 1.1: Add path info functions to paths.py
+- [x] Task 1.1: Add path info functions to paths.py [d237d3b]
   - WHERE: src/paths.py
   - WHAT: Add functions to get path resolution source (default/env/config)
   - HOW: Return tuple of (resolved_path, source)
   - SAFETY: New functions, no modifications
 
-- [ ] Task 1.2: Create path display helper
+- [x] Task 1.2: Create path display helper [d237d3b]
   - WHERE: src/paths.py
   - WHAT: Function to get all paths with resolution info
   - HOW: Returns dict of path_name -> (resolved, source)
@@ -18,25 +18,25 @@ Focus: Show current path resolution in GUI
 ## Phase 2: Context Hub Panel
 Focus: Add Path Configuration panel to GUI
 
-- [ ] Task 2.1: Add Paths tab to Context Hub
+- [x] Task 2.1: Add Paths tab to Context Hub [d237d3b]
   - WHERE: src/gui_2.py (Context Hub section)
   - WHAT: New tab/section for path configuration
   - HOW: Add ImGui tab item, follow existing panel patterns
   - SAFETY: New panel, no modifications to existing
 
-- [ ] Task 2.2: Display current paths
+- [x] Task 2.2: Display current paths [d237d3b]
   - WHERE: src/gui_2.py (new paths panel)
   - WHAT: Show resolved paths and their sources
   - HOW: Call paths.py functions, display in read-only text
   - SAFETY: New code
 
-- [ ] Task 2.3: Add path text inputs
+- [x] Task 2.3: Add path text inputs [d237d3b]
   - WHERE: src/gui_2.py (paths panel)
   - WHAT: Editable text inputs for each path
   - HOW: ImGui input_text for conductor_dir, logs_dir, scripts_dir
   - SAFETY: New code
 
-- [ ] Task 2.4: Add browse buttons
+- [x] Task 2.4: Add browse buttons [d237d3b]
   - WHERE: src/gui_2.py (paths panel)
   - WHAT: File dialog buttons to browse for directories
   - HOW: Use existing file dialog patterns in gui_2.py
@@ -45,19 +45,19 @@ Focus: Add Path Configuration panel to GUI
 ## Phase 3: Persistence
 Focus: Save path changes to config.toml
 
-- [ ] Task 3.1: Add config write function
+- [x] Task 3.1: Add config write function [d237d3b]
   - WHERE: src/gui_2.py or new utility
   - WHAT: Write [paths] section to config.toml
   - HOW: Read existing config, update paths section, write back
   - SAFETY: Backup before write, handle errors
 
-- [ ] Task 3.2: Add Apply button
+- [x] Task 3.2: Add Apply button [d237d3b]
   - WHERE: src/gui_2.py (paths panel)
   - WHAT: Button to save changes
   - HOW: Call config write function, show success/error message
   - SAFETY: Confirmation dialog
 
-- [ ] Task 3.3: Add Reset button
+- [x] Task 3.3: Add Reset button [d237d3b]
   - WHERE: src/gui_2.py (paths panel)
   - WHAT: Reset paths to defaults
   - HOW: Clear custom values, show confirmation
@@ -66,13 +66,13 @@ Focus: Save path changes to config.toml
 ## Phase 4: UX Polish
 Focus: Improve user experience
 
-- [ ] Task 4.1: Add restart warning
+- [x] Task 4.1: Add restart warning [d237d3b]
   - WHERE: src/gui_2.py (paths panel)
   - WHAT: Show warning that changes require restart
   - HOW: Text label after Apply
   - SAFETY: New code
 
-- [ ] Task 4.2: Add tooltips
+- [x] Task 4.2: Add tooltips [d237d3b]
   - WHERE: src/gui_2.py (paths panel)
   - WHAT: Explain each path and resolution order
   - HOW: ImGui set_tooltip on hover
@@ -81,7 +81,7 @@ Focus: Improve user experience
 ## Phase 5: Tests
 Focus: Verify GUI path configuration
 
-- [ ] Task 5.1: Test path display
+- [x] Task 5.1: Test path display [d237d3b]
   - WHERE: tests/test_gui_paths.py (new file)
   - WHAT: Verify paths panel shows correct values
   - HOW: Mock paths.py, verify display

conductor/archive/project_conductor_dir_20260308/plan.md

@@ -3,13 +3,13 @@
 ## Phase 1: Extend paths.py
 Focus: Add project-specific path resolution
 
-- [ ] Task 1.1: Add project-aware conductor path functions
+- [x] Task 1.1: Add project-aware conductor path functions [48e2ed8]
   - WHERE: src/paths.py
   - WHAT: Add optional project_path parameter to get_conductor_dir, get_tracks_dir, get_track_state_dir
   - HOW: If project_path provided, resolve relative to project root; otherwise use global
   - SAFETY: Maintain backward compatibility with no-arg calls
 
-- [ ] Task 1.2: Add project conductor path resolution
+- [x] Task 1.2: Add project conductor path resolution [48e2ed8]
   - WHERE: src/paths.py
   - WHAT: New function `_resolve_project_conductor_dir(project_path)` that reads from project TOML
   - HOW: Load project TOML, check `[conductor].dir` key
@@ -18,18 +18,18 @@ Focus: Add project-specific path resolution
 ## Phase 2: Update project_manager.py
 Focus: Use project-specific paths for track operations
 
-- [ ] Task 2.1: Update save_track_state to use project conductor dir
+- [x] Task 2.1: Update save_track_state to use project conductor dir [3999e9c]
   - WHERE: src/project_manager.py (around line 240)
   - WHAT: Pass project base_dir to paths.get_track_state_dir()
   - HOW: Get base_dir from project_path, call paths with project_path param
   - SAFETY: Maintain existing function signature compatibility
 
-- [ ] Task 2.2: Update load_track_state to use project conductor dir
+- [x] Task 2.2: Update load_track_state to use project conductor dir [3999e9c]
   - WHERE: src/project_manager.py (around line 252)
   - WHAT: Load track state from project-specific directory
   - HOW: Same as above
 
-- [ ] Task 2.3: Update get_all_tracks to use project conductor dir
+- [x] Task 2.3: Update get_all_tracks to use project conductor dir [3999e9c]
   - WHERE: src/project_manager.py (around line 297)
   - WHAT: List tracks from project-specific directory
   - HOW: Accept optional project_path param
@@ -37,7 +37,7 @@ Focus: Use project-specific paths for track operations
 ## Phase 3: Update app_controller.py
 Focus: Pass project path to track operations
 
-- [ ] Task 3.1: Update track creation to use project conductor dir
+- [x] Task 3.1: Update track creation to use project conductor dir [3999e9c]
   - WHERE: src/app_controller.py (around line 1907, 1937)
   - WHAT: Pass active_project_path to track path functions
   - HOW: Get active_project_path, pass to paths.get_tracks_dir()
@@ -46,13 +46,13 @@ Focus: Pass project path to track operations
 ## Phase 4: Tests
 Focus: Verify project-specific behavior
 
-- [ ] Task 4.1: Write test for project-specific conductor dir
+- [x] Task 4.1: Write test for project-specific conductor dir [48e2ed8]
   - WHERE: tests/test_project_paths.py (new file)
   - WHAT: Create mock project with custom conductor dir, verify tracks saved there
   - HOW: Mock project_manager, verify path resolution
   - SAFETY: New test file
 
-- [ ] Task 4.2: Test backward compatibility
+- [x] Task 4.2: Test backward compatibility [3999e9c]
   - WHERE: tests/test_project_paths.py
   - WHAT: Verify global paths still work without project_path
   - HOW: Call functions without project_path, verify defaults

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
@@ -33,7 +33,8 @@ 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.
-  - **Track-Scoped State Management:** Segregates discussion history and task progress into per-track state files (e.g., `conductor/tracks/<track_id>/state.toml`). This prevents global context pollution and ensures the Tech Lead session is isolated to the specific track's objective.
+    - **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).
 
   - **Programmable Execution State machine:** Governing the transition between "Auto-Queue" (autonomous worker spawning) and "Step Mode" (explicit manual approval for each task transition).
@@ -45,16 +46,24 @@ For deep implementation details when planning or implementing tracks, consult `d
 - **Parallel Multi-Agent Execution:** Executes multiple AI workers in parallel using a non-blocking execution engine and a dedicated `WorkerPool`. Features configurable concurrency limits (defaulting to 4) to optimize resource usage and prevent API rate limiting.
 - **Parallel Tool Execution:** Executes independent tool calls (e.g., parallel file reads) concurrently within a single agent turn using an asynchronous execution engine, significantly reducing end-to-end latency.
 - **Automated Tier 4 QA:** Integrates real-time error interception in the shell runner, automatically forwarding technical failures to cheap sub-agents for 20-word diagnostic summaries injected back into the worker history.
+- **External MCP Server Support:** Adds support for integrating external Model Context Protocol (MCP) servers, expanding the agent's toolset with the broader MCP ecosystem.
+  - **Multi-Server Lifecycle Management:** Orchestrates multiple concurrent MCP server sessions (Stdio for local subprocesses and SSE for remote servers).
+  - **Flexible Configuration:** Supports global (`config.toml`) and project-specific (`manual_slop.toml`) paths for `mcp_config.json` (standard MCP configuration format).
+  - **Auto-Start & Discovery:** Automatically initializes configured servers on project load and dynamically aggregates their tools into the agent's capability declarations.
+  - **Dedicated Operations UI:** Features a new **External Tools** section within the Operations Hub for monitoring server status (idle, starting, running, error) and browsing discovered tool schemas. Supports **Pop-Out Panel functionality**, allowing the External Tools interface to be detached into a standalone window for optimized multi-monitor workflows.
+  - **Strict HITL Safety:** All external tool calls are intercepted and require explicit human-in-the-loop approval via the standard confirmation dialog before execution.
 - **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.
 - **Improved MMA Observability:** Enhances sub-agent logging by injecting precise ticket IDs and descriptive roles into communication metadata, enabling granular filtering and tracking of parallel worker activities within the Comms History.
 - **In-Depth Toolset Access:** MCP-like file exploration, URL fetching, search, and dynamic context aggregation embedded within a multi-viewport Dear PyGui/ImGui interface.
-- **Integrated Workspace:** A consolidated Hub-based layout (Context, AI Settings, Discussion, Operations) designed for expert multi-monitor workflows.
+- **Integrated Workspace:** A consolidated Hub-based layout (Context, AI Settings, Discussion, Operations) designed for expert multi-monitor workflows. Features **GUI-Based Path Configuration** within the Context Hub, allowing users to view and edit system paths (conductor, logs, scripts) with real-time resolution source tracking (default, env, or config). Changes are applied immediately at runtime without requiring an application restart.
 - **Session Analysis:** Ability to load and visualize historical session logs with a dedicated tinted "Prior Session" viewing mode.
 - **Structured Log Taxonomy:** Automated session-based log organization into configurable directories (defaulting to `logs/sessions/`). Includes a dedicated GUI panel for monitoring and manual whitelisting. Features an intelligent heuristic-based pruner that automatically cleans up insignificant logs older than 24 hours while preserving valuable sessions.
 - **Clean Project Root:** Enforces a "Cruft-Free Root" policy by organizing core implementation into a `src/` directory and redirecting all temporary test data, configurations, and AI-generated artifacts to `tests/artifacts/`.
@@ -63,7 +72,7 @@ For deep implementation details when planning or implementing tracks, consult `d
 - **Professional UI Theme & Typography:** Implements a high-fidelity visual system featuring **Inter** and **Maple Mono** fonts for optimal readability. Employs a cohesive "Subtle Rounding" aesthetic across all standard widgets, supported by custom **soft shadow shaders** for modals and popups to provide depth and professional polish. Includes a selectable **NERV UI theme** featuring a "Black Void" palette, zero-rounding geometry, and CRT-style visual effects (scanlines, status flickering).
 - **Rich Text & Syntax Highlighting:** Provides advanced rendering for messages, logs, and tool outputs using a hybrid Markdown system. Supports GitHub-Flavored Markdown (GFM) via `imgui_markdown` and integrates `ImGuiColorTextEdit` for high-performance syntax highlighting of code blocks (Python, JSON, C++, etc.). Includes automated language detection and clickable URL support.
 - **Multi-Viewport & Layout Management:** Full support for ImGui Multi-Viewport, allowing users to detach panels into standalone OS windows for complex multi-monitor workflows. Includes a comprehensive **Layout Presets system**, enabling developers to save, name, and instantly restore custom window arrangements, including their Multi-Viewport state.
-- **Headless Backend Service:** Optional headless mode allowing the core AI and tool execution logic to run as a decoupled REST API service (FastAPI), optimized for Docker and server-side environments (e.g., Unraid).
+- **Headless Backend Service & Hook API:** Optional headless mode allowing the core AI and tool execution logic to run as a decoupled service. Features a comprehensive Hook API and WebSocket event streaming for remote orchestration, deep state inspection, and manual worker lifecycle management.
 - **Remote Confirmation Protocol:** A non-blocking, ID-based challenge/response mechanism for approving AI actions via the REST API, enabling remote "Human-in-the-Loop" safety.
 - **Gemini CLI Integration:** Allows using the `gemini` CLI as a headless backend provider. This enables leveraging Gemini subscriptions with advanced features like persistent sessions, while maintaining full "Human-in-the-Loop" safety through a dedicated bridge for synchronous tool call approvals within the Manual Slop GUI. Now features full functional parity with the direct API, including accurate token estimation, safety settings, and robust system instruction handling.
 - **Context & Token Visualization:** Detailed UI panels for monitoring real-time token usage, history depth, and **visual cache awareness** (tracking specific files currently live in the provider's context cache).

conductor/tech-stack.md

@@ -12,6 +12,7 @@
 ## Web & Service Frameworks
 
 - **FastAPI:** High-performance REST API framework for providing the headless backend service.
+- **websockets:** Lightweight asynchronous WebSocket server for real-time event streaming and remote orchestration.
 - **Uvicorn:** ASGI server for serving the FastAPI application.
 
 ## AI Integration SDKs
@@ -29,7 +30,7 @@
 
 - **ai_style_formatter.py:** Custom Python formatter specifically designed to enforce 1-space indentation and ultra-compact whitespace to minimize token consumption.
 
-- **src/paths.py:** Centralized module for path resolution, allowing directory paths (logs, conductor, scripts) to be configured via `config.toml` or environment variables, eliminating hardcoded filesystem dependencies.
+- **src/paths.py:** Centralized module for path resolution. Supports project-specific conductor directory overrides via project TOML (`[conductor].dir`), enabling isolated track management per project. If not specified, conductor paths default to `./conductor` relative to each project's TOML file. All paths are resolved to absolute objects. Provides **Path Resolution Metadata**, exposing the source of each resolved path (default, environment variable, or configuration file) for high-fidelity GUI display. Supports **Runtime Re-Resolution** via `reset_resolved()`, allowing path changes to be applied immediately without an application restart. Path configuration (logs, scripts) can also be configured via `config.toml` or environment variables, eliminating hardcoded filesystem dependencies.
 
 - **src/presets.py:** Implements `PresetManager` for high-performance CRUD operations on system prompt presets stored in TOML format (`presets.toml`, `project_presets.toml`). Supports dynamic path resolution and scope-based inheritance.
 
@@ -39,6 +40,10 @@
 
 - **src/tool_presets.py:** Extends `ToolPresetManager` to handle nested `Tool` models, weights, and global `BiasProfile` persistence within `tool_presets.toml`.
 
+- **src/mcp_client.py (External Extension):** Implements the `ExternalMCPManager` for orchestrating third-party Model Context Protocol servers.
+  - **StdioMCPServer:** Manages local MCP servers via asynchronous subprocess pipes (stdin/stdout/stderr).
+  - **RemoteMCPServer (SSE):** Provides a foundation for remote MCP integration via Server-Sent Events.
+  - **JSON-RPC 2.0 Engine:** Handles asynchronous message routing, request/response matching, and error handling for all external MCP communication.
 
 - **tree-sitter / AST Parsing:** For deterministic AST parsing and automated generation of curated "Skeleton Views" and "Targeted Views" (extracting specific functions and their dependencies). Features an integrated AST cache with mtime-based invalidation to minimize re-parsing overhead.
 - **pydantic / dataclasses:** For defining strict state schemas (Tracks, Tickets) used in linear orchestration.
@@ -47,6 +52,8 @@
 - **LogRegistry & LogPruner:** Custom components for session metadata persistence and automated filesystem cleanup within the `logs/sessions/` taxonomy.
 - **psutil:** For system and process monitoring (CPU/Memory telemetry).
 - **uv:** An extremely fast Python package and project manager.
+- **PyOpenGL:** For compiling and executing true GLSL shaders (dynamic backgrounds, CRT post-processing) directly on the GPU.
+- **pywin32:** For custom OS window frame manipulation on Windows (e.g., minimizing, maximizing, closing, and dragging the borderless ImGui window).
 - **pytest:** For unit and integration testing, leveraging custom fixtures for live GUI verification.
 - **Taxonomy & Artifacts:** Enforces a clean root by organizing core implementation into a `src/` directory, and redirecting session logs and artifacts to configurable directories (defaulting to `logs/sessions/` and `scripts/generated/`). Temporary test data and test logs are siloed in `tests/artifacts/` and `tests/logs/`.
 - **ApiHookClient:** A dedicated IPC client for automated GUI interaction and state inspection.
@@ -63,6 +70,6 @@
 - **Synchronous IPC Approval Flow:** A specialized bridge mechanism that allows headless AI providers (like Gemini CLI) to synchronously request and receive human approval for tool calls via the GUI's REST API hooks.
 - **High-Fidelity Selectable Labels:** Implements a pattern for making read-only UI text selectable by wrapping `imgui.input_text` with `imgui.InputTextFlags_.read_only`. Includes a specialized `_render_selectable_label` helper that resets frame backgrounds, borders, and padding to mimic standard labels while enabling OS-level clipboard support (Ctrl+C).
 - **Hybrid Markdown Rendering:** Employs a custom `MarkdownRenderer` that orchestrates `imgui_markdown` for standard text and headers while intercepting code blocks to render them via cached `ImGuiColorTextEdit` instances. This ensures high-performance rich text rendering with robust syntax highlighting and stateful text selection.
-- **Faux-Shader Visual Effects:** Utilizes an optimized `ImDrawList`-based batching technique to simulate advanced visual effects such as soft shadows, acrylic glass overlays, and **CRT scanline overlays** without the overhead of heavy GPU-resident shaders or external OpenGL dependencies. Includes support for **dynamic status flickering** and **alert pulsing** integrated into the NERV theme.
+- **Hybrid Shader Pipeline:** Utilizes an optimized `ImDrawList`-based batching technique to simulate UI effects such as soft shadows and acrylic glass overlays without the overhead of heavy GPU-resident shaders. Supplemented by a true GPU shader pipeline using `PyOpenGL` and Framebuffer Objects (FBOs) for complex post-processing (CRT scanlines, bloom) and dynamic backgrounds.
 - **Interface-Driven Development (IDD):** Enforces a "Stub-and-Resolve" pattern where cross-module dependencies are resolved by generating signatures/contracts before implementation.
 

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.
 
@@ -10,32 +10,42 @@ This file tracks all major tracks for the project. Each track has its own detail
 
 ### Architecture & Backend
 
-1. [ ] **Track: External MCP Server Support**
-   *Link: [./tracks/external_mcp_support_20260308/](./tracks/external_mcp_support_20260308/)*
-   *Goal: Add support for external MCP servers (Local Stdio and Remote SSE/WS) with flexible configuration and lifecycle management (including auto-start on project load).*
-
-2. [ ] **Track: RAG Support**
+1. [ ] **Track: RAG Support**
    *Link: [./tracks/rag_support_20260308/](./tracks/rag_support_20260308/)*
    *Goal: Add support for RAG (Retrieval-Augmented Generation) using local vector stores (Chroma/Qdrant), native vendor retrieval, and external RAG APIs. Implement indexing pipeline and retrieval UI.*
 
-3. [x] **Track: Agent Tool Preference & Bias Tuning**
+2. [x] **Track: Agent Tool Preference & Bias Tuning**
    *Link: [./tracks/tool_bias_tuning_20260308/](./tracks/tool_bias_tuning_20260308/)*
    *Goal: Influence agent tool selection via a weighting system. Implement semantic nudges in tool descriptions and a dynamic "Tooling Strategy" section in the system prompt. Includes GUI badges and sliders for weight adjustment.*
 
-4. [~] **Track: Expanded Hook API & Headless Orchestration**
+3. [x] **Track: Expanded Hook API & Headless Orchestration**
    *Link: [./tracks/hook_api_expansion_20260308/](./tracks/hook_api_expansion_20260308/)*
    *Goal: Maximize internal state exposure and provide comprehensive control endpoints (worker spawn/kill, pipeline pause/resume, DAG mutation) via the Hook API. Implement WebSocket-based real-time event streaming.*
 
-5. [ ] **Track: Codebase Audit and Cleanup**
+4. [ ] **Track: Codebase Audit and Cleanup**
     *Link: [./tracks/codebase_audit_20260308/](./tracks/codebase_audit_20260308/)*
 
-6. [ ] **Track: Expanded Test Coverage and Stress Testing**
+5. [ ] **Track: Expanded Test Coverage and Stress Testing**
    *Link: [./tracks/test_coverage_expansion_20260309/](./tracks/test_coverage_expansion_20260309/)*
 
-7. [ ] **Track: Beads Mode Integration**
+6. [ ] **Track: Beads Mode Integration**
    *Link: [./tracks/beads_mode_20260309/](./tracks/beads_mode_20260309/)*
    *Goal: Integrate Beads (git-backed graph issue tracker) as an alternative backend for MMA implementation tracks and tickets.*
 
+7. [ ] **Track: Optimization pass for Data-Oriented Python heuristics**
+    *Link: [./tracks/data_oriented_optimization_20260312/](./tracks/data_oriented_optimization_20260312/)*
+
+ 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.*
+
 ---
 
 ### GUI Overhauls & Visualizations
@@ -58,25 +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. [x] **Track: Advanced Text Viewer with Syntax Highlighting**
+    *Link: [./tracks/text_viewer_rich_rendering_20260313/](./tracks/text_viewer_rich_rendering_20260313/)*
+
 ---
 
 ### Additional Language Support
@@ -103,18 +120,6 @@ This file tracks all major tracks for the project. Each track has its own detail
 
 ---
 
-### Path Configuration
-
-1. [ ] **Track: Project-Specific Conductor Directory**
-   *Link: [./tracks/project_conductor_dir_20260308/](./tracks/project_conductor_dir_20260308/)*
-   *Goal: Make conductor directory per-project. Each project TOML can specify custom conductor dir for isolated track/state management.*
-
-2. [ ] **Track: GUI Path Configuration in Context Hub**
-   *Link: [./tracks/gui_path_config_20260308/](./tracks/gui_path_config_20260308/)*
-   *Goal: Add path configuration UI to Context Hub. Allow users to view and edit configurable paths directly from the GUI.*
-
----
-
 ### Manual UX Controls
 
 1. [x] **Track: Saved System Prompt Presets**
@@ -168,6 +173,13 @@ 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)
 - [x] **Track: True Parallel Worker Execution (The DAG Realization)**
 - [x] **Track: Deep AST-Driven Context Pruning (RAG for Code)**
 - [x] **Track: Visual DAG & Interactive Ticket Editing**

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/custom_shaders_20260309/plan.md

@@ -1,35 +1,35 @@
 # Implementation Plan: Custom Shader and Window Frame Support
 
-## Phase 1: Investigation & Architecture Prototyping
-- [ ] Task: Investigate `imgui-bundle` and Dear PyGui capabilities for injecting raw custom shaders (OpenGL/D3D11) vs extending ImDrawList batching.
-- [ ] Task: Investigate Python ecosystem capabilities for overloading OS window frames (e.g., `pywin32` for DWM vs ImGui borderless mode).
-- [ ] Task: Draft architectural design document (`docs/guide_shaders_and_window.md`) detailing the chosen shader injection method and window frame overloading strategy.
-- [ ] Task: Conductor - User Manual Verification 'Phase 1: Investigation & Architecture Prototyping' (Protocol in workflow.md)
+## Phase 1: Investigation & Architecture Prototyping [checkpoint: 815ee55]
+- [x] Task: Investigate imgui-bundle and Dear PyGui capabilities for injecting raw custom shaders (OpenGL/D3D11) vs extending ImDrawList batching. [5f4da36]
+- [x] Task: Investigate Python ecosystem capabilities for overloading OS window frames (e.g., `pywin32` for DWM vs ImGui borderless mode). [5f4da36]
+- [x] Task: Draft architectural design document (`docs/guide_shaders_and_window.md`) detailing the chosen shader injection method and window frame overloading strategy. [5f4da36]
+- [x] Task: Conductor - User Manual Verification 'Phase 1: Investigation & Architecture Prototyping' (Protocol in workflow.md) [815ee55]
 
-## Phase 2: Custom OS Window Frame Implementation
-- [ ] Task: Write Tests: Verify the application window launches with the custom frame/borderless mode active.
-- [ ] Task: Implement: Integrate custom window framing logic into the main GUI loop (`src/gui_2.py` / Dear PyGui setup).
-- [ ] Task: Write Tests: Verify standard window controls (minimize, maximize, close, drag) function correctly with the new frame.
-- [ ] Task: Implement: Add custom title bar and window controls matching the application's theme.
-- [ ] Task: Conductor - User Manual Verification 'Phase 2: Custom OS Window Frame Implementation' (Protocol in workflow.md)
+## Phase 2: Custom OS Window Frame Implementation [checkpoint: b9ca69f]
+- [x] Task: Write Tests: Verify the application window launches with the custom frame/borderless mode active. [02fca1f]
+- [x] Task: Implement: Integrate custom window framing logic into the main GUI loop (`src/gui_2.py` / Dear PyGui setup). [59d7368]
+- [x] Task: Write Tests: Verify standard window controls (minimize, maximize, close, drag) function correctly with the new frame. [59d7368]
+- [x] Task: Implement: Add custom title bar and window controls matching the application's theme. [59d7368]
+- [x] Task: Conductor - User Manual Verification 'Phase 2: Custom OS Window Frame Implementation' (Protocol in workflow.md) [b9ca69f]
 
-## Phase 3: Core Shader Pipeline Integration
-- [ ] Task: Write Tests: Verify the shader manager class initializes without errors and can load a basic shader program.
-- [ ] Task: Implement: Create `src/shader_manager.py` (or extend `src/shaders.py`) to handle loading, compiling, and binding true GPU shaders or advanced Faux-Shaders.
-- [ ] Task: Write Tests: Verify shader uniform data can be updated from Python dictionaries/TOML configurations.
-- [ ] Task: Implement: Add support for uniform passing (time, resolution, mouse pos) to the shader pipeline.
-- [ ] Task: Conductor - User Manual Verification 'Phase 3: Core Shader Pipeline Integration' (Protocol in workflow.md)
+## Phase 3: Core Shader Pipeline Integration [checkpoint: 5ebce89]
+- [x] Task: Write Tests: Verify the shader manager class initializes without errors and can load a basic shader program. [ac4f63b]
+- [x] Task: Implement: Create `src/shader_manager.py` (or extend `src/shaders.py`) to handle loading, compiling, and binding true GPU shaders or advanced Faux-Shaders. [ac4f63b]
+- [x] Task: Write Tests: Verify shader uniform data can be updated from Python dictionaries/TOML configurations. [0938396]
+- [x] Task: Implement: Add support for uniform passing (time, resolution, mouse pos) to the shader pipeline. [0938396]
+- [x] Task: Conductor - User Manual Verification 'Phase 3: Core Shader Pipeline Integration' (Protocol in workflow.md) [5ebce89]
 
-## Phase 4: Specific Shader Implementations (CRT, Post-Process, Backgrounds)
-- [ ] Task: Write Tests: Verify background shader logic can render behind the main ImGui layer.
-- [ ] Task: Implement: Add "Dynamic Background" shader implementation (e.g., animated noise/gradients).
-- [ ] Task: Write Tests: Verify post-process shader logic can capture the ImGui output and apply an effect over it.
-- [ ] Task: Implement: Add "CRT / Retro" (NERV theme) and general "Post-Processing" (bloom/blur) shaders.
-- [ ] Task: Conductor - User Manual Verification 'Phase 4: Specific Shader Implementations' (Protocol in workflow.md)
+## Phase 4: Specific Shader Implementations (CRT, Post-Process, Backgrounds) [checkpoint: 50f98de]
+- [x] Task: Write Tests: Verify background shader logic can render behind the main ImGui layer. [836168a]
+- [x] Task: Implement: Add "Dynamic Background" shader implementation (e.g., animated noise/gradients). [836168a]
+- [x] Task: Write Tests: Verify post-process shader logic can capture the ImGui output and apply an effect over it. [905ac00]
+- [x] Task: Implement: Add "CRT / Retro" (NERV theme) and general "Post-Processing" (bloom/blur) shaders. [905ac00]
+- [x] Task: Conductor - User Manual Verification 'Phase 4: Specific Shader Implementations' (Protocol in workflow.md) [50f98de]
 
-## Phase 5: Configuration and Live Editor UI
-- [ ] Task: Write Tests: Verify shader and window frame settings can be parsed from `config.toml`.
-- [ ] Task: Implement: Update `src/theme.py` / `src/project_manager.py` to parse and apply shader/window configurations from TOML.
-- [ ] Task: Write Tests: Verify the Live UI Editor panel renders and modifying its values updates the shader uniforms.
-- [ ] Task: Implement: Create a "Live UI Editor" Dear PyGui/ImGui panel to tweak shader uniforms in real-time.
-- [ ] Task: Conductor - User Manual Verification 'Phase 5: Configuration and Live Editor UI' (Protocol in workflow.md)
+## Phase 5: Configuration and Live Editor UI [checkpoint: da47819]
+- [x] Task: Write Tests: Verify shader and window frame settings can be parsed from `config.toml`. [d69434e]
+- [x] Task: Implement: Update `src/theme.py` / `src/project_manager.py` to parse and apply shader/window configurations from TOML. [d69434e]
+- [x] Task: Write Tests: Verify the Live UI Editor panel renders and modifying its values updates the shader uniforms. [229fbe2]
+- [x] Task: Implement: Create a "Live UI Editor" Dear PyGui/ImGui panel to tweak shader uniforms in real-time. [229fbe2]
+- [x] Task: Conductor - User Manual Verification 'Phase 5: Configuration and Live Editor UI' (Protocol in workflow.md) [da47819]

conductor/tracks/data_oriented_optimization_20260312/index.md

@@ -0,0 +1,5 @@
+# Track data_oriented_optimization_20260312 Context
+
+- [Specification](./spec.md)
+- [Implementation Plan](./plan.md)
+- [Metadata](./metadata.json)

conductor/tracks/data_oriented_optimization_20260312/metadata.json

@@ -0,0 +1,8 @@
+{
+  "track_id": "data_oriented_optimization_20260312",
+  "type": "chore",
+  "status": "new",
+  "created_at": "2026-03-12T00:00:00Z",
+  "updated_at": "2026-03-12T00:00:00Z",
+  "description": "Optimization pass. I want to update the product guidlines to take into account with data-oriented appraoch the more performant way to semantically define procedrual code in python so executes almost entirely heavy operations optimally. I know there is a philosophy of 'the less python does the better' which is problably why the imgui lib is so performant because all python really does is define the ui's DAG via an imgui interface procedurally along with what state the dag may modify within its constraints of interactions the user may do. This problably can be reflected in the way the rest of the codebase is done. I want to go over the ./src and ./simulation to make sure this insight and related herustics are properly enfroced. Worst case I want to identify what code I should consider lower down to C maybe and making python bindings to if there is a significant bottleneck identified via profiling and testing that cannot be resolved otherwise."
+}

conductor/tracks/data_oriented_optimization_20260312/plan.md

@@ -0,0 +1,27 @@
+# Implementation Plan: Data-Oriented Python Optimization Pass
+
+## Phase 1: Guidelines and Instrumentation
+- [ ] Task: Update `conductor/product-guidelines.md` with Data-Oriented Python heuristics and the "less Python does the better" philosophy.
+- [ ] Task: Review existing profiling instrumentation in `src/performance_monitor.py` or diagnostic hooks.
+- [ ] Task: Expand profiling instrumentation to capture more detailed execution times for non-GUI data structures/processes if necessary.
+- [ ] Task: Conductor - User Manual Verification 'Phase 1: Guidelines and Instrumentation' (Protocol in workflow.md)
+
+## Phase 2: Audit and Profiling (`src/` and `simulation/`)
+- [ ] Task: Run profiling scenarios (especially utilizing simulations) to generate baseline metrics.
+- [ ] Task: Audit `src/` (e.g., `dag_engine.py`, `multi_agent_conductor.py`, `aggregate.py`) against the new guidelines, cross-referencing with profiling data to identify bottlenecks.
+- [ ] Task: Audit `simulation/` files against the new guidelines to ensure the test harness is performant and non-blocking.
+- [ ] Task: Compile a list of identified bottleneck targets to refactor.
+- [ ] Task: Conductor - User Manual Verification 'Phase 2: Audit and Profiling (`src/` and `simulation/`)' (Protocol in workflow.md)
+
+## Phase 3: Targeted Optimization and Refactoring
+- [ ] Task: Write/update tests for the first identified bottleneck to establish a performance or structural baseline (Red Phase).
+- [ ] Task: Refactor the first identified bottleneck to align with data-oriented guidelines (Green Phase).
+- [ ] Task: Write/update tests for remaining identified bottlenecks.
+- [ ] Task: Refactor remaining identified bottlenecks.
+- [ ] Task: Conductor - User Manual Verification 'Phase 3: Targeted Optimization and Refactoring' (Protocol in workflow.md)
+
+## Phase 4: Final Evaluation and Documentation
+- [ ] Task: Re-run all profiling scenarios to compare against the baseline metrics.
+- [ ] Task: Analyze remaining bottlenecks that did not reach performance thresholds and document them as candidates for C/C++ bindings (Last Resort).
+- [ ] Task: Generate a final summary report of the optimizations applied and the C extension evaluation.
+- [ ] Task: Conductor - User Manual Verification 'Phase 4: Final Evaluation and Documentation' (Protocol in workflow.md)

conductor/tracks/data_oriented_optimization_20260312/spec.md

@@ -0,0 +1,35 @@
+# Specification: Data-Oriented Python Optimization Pass
+
+## Overview
+Perform an optimization pass and audit across the codebase (`./src` and `./simulation`), aligning the implementation with the Data-Oriented Design philosophy and the "less Python does the better" heuristic. Update the `product-guidelines.md` to formally document this approach for procedural Python code.
+
+## Functional Requirements
+1. **Update Product Guidelines:**
+   - Formalize the heuristic that Python should act primarily as a procedural semantic definer (similar to how ImGui defines a UI DAG), delegating heavy lifting.
+   - Enforce data-oriented guidelines for Python code structure, focusing on minimizing Python JIT overhead.
+2. **Codebase Audit (`./src` and `./simulation`):**
+   - Review global `src/` files and simulation logic against the new guidelines.
+   - Identify bottlenecks that violate these heuristics (e.g., heavy procedural state manipulation in Python).
+3. **Profiling & Instrumentation Expansion:**
+   - Expand existing profiling instrumentation (e.g., `performance_monitor.py` or diagnostic hooks) if currently insufficient for identifying real structural bottlenecks.
+4. **Optimization Execution:**
+   - Refactor identified bottlenecks to align with the new data-oriented Python heuristics.
+   - Re-evaluate performance post-refactor.
+5. **C Extension Evaluation (Last Resort):**
+   - If Python optimizations fail to meet performance thresholds, specifically identify and document routines that must be lowered to C/C++ with Python bindings. Only proceed with bindings if absolutely necessary.
+
+## Non-Functional Requirements
+- Maintain existing test coverage and strict type-hinting requirements.
+- Ensure 1-space indentation and ultra-compact style rules are not violated during refactoring.
+- Ensure the main GUI rendering thread is never blocked.
+
+## Acceptance Criteria
+- `product-guidelines.md` is updated with data-oriented procedural Python guidelines.
+- `src/` and `simulation/` undergo a documented profiling audit.
+- Identified bottlenecks are refactored to reduce Python overhead.
+- No regressions in automated simulation or unit tests.
+- A final report is provided detailing optimizations made and any candidates for future C extension porting.
+
+## Out of Scope
+- Actually implementing C/C++ bindings in this track (this track only identifies/evaluates them as a last resort; if needed, they get a separate track).
+- Major UI visual theme changes.

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 [checkpoint: a3c8d4b]
+Focus: Per-discussion file filter with save/load preset functionality
+
+- [x] Task: Write tests for Context Composition state management [a3c8d4b]
+- [x] Task: Create _render_context_composition_panel method [a3c8d4b]
+- [x] Task: Implement file/screenshot selection display (filtered from Files & Media) [a3c8d4b]
+- [x] Task: Implement per-file flags display (Auto-Aggregate, Force Full) [a3c8d4b]
+- [x] Task: Implement Save as Preset / Load Preset buttons [a3c8d4b]
+- [x] Task: Connect Context Presets storage to this panel [a3c8d4b]
+- [ ] Task: Update Persona editor to reference Context Composition presets (NOTE: already done via existing context_preset field in Persona)
+- [x] Task: Write tests for Context Composition preset save/load [a3c8d4b]
+- [x] Task: Conductor - User Manual Verification 'Phase 3: Context Composition Tab'
+
+## Phase 4: Takes Timeline Integration [checkpoint: cc6a651]
+Focus: DAW-style branching with proper visual timeline and synthesis
+
+- [x] Task: Audit existing takes data structure and synthesis_formatter [documented above]
+- [ ] Task: Enhance takes data model with parent_entry and parent_take tracking (deferred - existing model sufficient)
+- [x] Task: Implement Branch from Entry action in discussion history [already existed]
+- [x] Task: Implement visual timeline showing take divergence [_render_takes_panel with table view]
+- [x] Task: Integrate synthesis panel into Takes tab [cc6a651]
+- [x] Task: Implement take selection for synthesis [cc6a651]
+- [x] Task: Write tests for take branching and synthesis [cc6a651]
+- [x] 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/external_mcp_support_20260308/plan.md

@@ -1,42 +0,0 @@
-# Implementation Plan: External MCP Server Support
-
-## Phase 1: Configuration & Data Modeling
-- [ ] Task: Define the schema for external MCP server configuration.
-    - [ ] Update `src/models.py` to include `MCPServerConfig` and `MCPConfiguration` classes.
-    - [ ] Implement logic to load `mcp_config.json` from global and project-specific paths.
-- [ ] Task: Integrate configuration loading into `AppController`.
-    - [ ] Ensure the MCP config path is correctly resolved from `config.toml` and `manual_slop.toml`.
-- [ ] Task: Write unit tests for configuration loading and validation.
-- [ ] Task: Conductor - User Manual Verification 'Phase 1: Configuration & Data Modeling' (Protocol in workflow.md)
-
-## Phase 2: MCP Client Extension
-- [ ] Task: Implement `ExternalMCPManager` in `src/mcp_client.py`.
-    - [ ] Add support for managing multiple MCP server sessions.
-    - [ ] Implement the `StdioMCPClient` for local subprocess communication.
-    - [ ] Implement the `RemoteMCPClient` for SSE/WebSocket communication.
-- [ ] Task: Update Tool Discovery.
-    - [ ] Implement `list_external_tools()` to aggregate tools from all active external servers.
-- [ ] Task: Update Tool Dispatch.
-    - [ ] Modify `mcp_client.dispatch()` and `mcp_client.async_dispatch()` to route tool calls to either native tools or the appropriate external server.
-- [ ] Task: Write integration tests for stdio and remote MCP client communication (using mock servers).
-- [ ] Task: Conductor - User Manual Verification 'Phase 2: MCP Client Extension' (Protocol in workflow.md)
-
-## Phase 3: GUI Integration & Lifecycle
-- [ ] Task: Update the **Operations** panel in `src/gui_2.py`.
-    - [ ] Create a new "External Tools" section.
-    - [ ] List discovered tools from active external servers.
-    - [ ] Add a "Refresh External MCPs" button to reload configuration and rediscover tools.
-- [ ] Task: Implement Lifecycle Management.
-    - [ ] Add the "Auto-start on Project Load" logic to start servers when a project is initialized.
-    - [ ] Add status indicators (e.g., color-coded dots) for each external server in the GUI.
-- [ ] Task: Write visual regression tests or simulation scripts to verify the updated Operations panel.
-- [ ] Task: Conductor - User Manual Verification 'Phase 3: GUI Integration & Lifecycle' (Protocol in workflow.md)
-
-## Phase 4: Agent Integration & HITL
-- [ ] Task: Update AI tool declarations.
-    - [ ] Ensure `ai_client.py` includes external tools in the tool definitions sent to Gemini/Anthropic.
-- [ ] Task: Verify HITL Approval Flow.
-    - [ ] Ensure that calling an external tool correctly triggers the `ConfirmDialog` modal.
-    - [ ] Verify that approved external tool results are correctly returned to the AI.
-- [ ] Task: Perform a final end-to-end verification with a real external MCP server.
-- [ ] Task: Conductor - User Manual Verification 'Phase 4: Agent Integration & HITL' (Protocol in workflow.md)

conductor/tracks/hook_api_expansion_20260308/plan.md

@@ -41,4 +41,4 @@
     - [x] Create a specialized simulation script that replicates a full MMA track lifecycle (planning, worker spawn, DAG mutation, completion) using ONLY the Hook API.
 - [x] Task: Final performance audit.
     - [x] Ensure that active WebSocket clients and large state dumps do not cause GUI frame drops.
-- [ ] Task: Conductor - User Manual Verification 'Phase 4: Headless Refinement & Verification' (Protocol in workflow.md)
+- [x] Task: Conductor - User Manual Verification 'Phase 4: Headless Refinement & Verification' (Protocol in workflow.md)

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/index.md

@@ -0,0 +1,5 @@
+# Track text_viewer_rich_rendering_20260313 Context
+
+- [Specification](./spec.md)
+- [Implementation Plan](./plan.md)
+- [Metadata](./metadata.json)

conductor/tracks/text_viewer_rich_rendering_20260313/metadata.json

@@ -0,0 +1,8 @@
+{
+  "track_id": "text_viewer_rich_rendering_20260313",
+  "type": "feature",
+  "status": "new",
+  "created_at": "2026-03-13T14:22:00Z",
+  "updated_at": "2026-03-13T14:22:00Z",
+  "description": "Make the text viewer support syntax highlighting and markdown for different text types. Whatever feeds the text viewer new context must specify the type to use otherwise fallback to just regular text visualization without highlighting or markdown rendering."
+}

conductor/tracks/text_viewer_rich_rendering_20260313/plan.md

@@ -0,0 +1,29 @@
+# Implementation Plan: Advanced Text Viewer with Syntax Highlighting
+
+## Phase 1: State & Interface Update
+- [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)
+- [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)
+- [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
+- [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/text_viewer_rich_rendering_20260313/spec.md

@@ -0,0 +1,30 @@
+# Specification: Advanced Text Viewer with Syntax Highlighting
+
+## Overview
+Enhance the existing "Text Viewer" popup panel in the Manual Slop GUI to support rich rendering, including syntax highlighting for various code types and Markdown rendering. The viewer will transition from a basic text/multiline input to a specialized component leveraging the project's hybrid rendering pattern.
+
+## Functional Requirements
+- **Rich Rendering Support:**
+  - **Code:** Integration with `ImGuiColorTextEdit` for syntax highlighting (Python, PowerShell, JSON, TOML, etc.).
+  - **Markdown:** Integration with `imgui_markdown` for rendering formatted text and documents.
+  - **Fallback:** Plain text rendering for unknown or unspecified types.
+- **Explicit Type Specification:**
+  - The component/function triggering the viewer (e.g., `_render_text_viewer`) must provide an explicit `text_type` parameter (e.g., "python", "markdown", "text").
+- **Enhanced UI Features:**
+  - **Line Numbers:** Display line numbers in the gutter when viewing code.
+  - **Copy Button:** A dedicated button to copy the entire content to the clipboard.
+  - **Independent Word Wrap:** A toggle within the viewer window to enable/disable word wrapping specifically for that instance, overriding the global GUI setting if necessary.
+  - **Persistent Sizing:** The viewer should maintain its size/position via ImGui's standard `.ini` persistence.
+
+## Technical Implementation
+- Update `App` state in `src/gui_2.py` to store `text_viewer_type`.
+- Modify `_render_text_viewer` signature to accept `text_type`.
+- Update the rendering loop in `_gui_func` to switch between `MarkdownRenderer` logic and `TextEditor` logic based on `text_viewer_type`.
+- Ensure proper caching of `TextEditor` instances to maintain scroll position and selection state while the viewer is open.
+
+## Acceptance Criteria
+- [ ] Clicking a preview button for a Python file opens the viewer with syntax highlighting and line numbers.
+- [ ] Clicking a preview for a `.md` file renders it as formatted Markdown.
+- [ ] The "Copy" button correctly copies text to the OS clipboard.
+- [ ] The word wrap toggle works immediately without affecting other panels.
+- [ ] Unsupported types gracefully fall back to standard plain text.

conductor/tracks/thinking_trace_handling_20260313/index.md

@@ -0,0 +1,5 @@
+# Track thinking_trace_handling_20260313 Context
+
+- [Specification](./spec.md)
+- [Implementation Plan](./plan.md)
+- [Metadata](./metadata.json)

conductor/tracks/thinking_trace_handling_20260313/metadata.json

@@ -0,0 +1,8 @@
+{
+  "track_id": "thinking_trace_handling_20260313",
+  "type": "feature",
+  "status": "new",
+  "created_at": "2026-03-13T13:28:00Z",
+  "updated_at": "2026-03-13T13:28:00Z",
+  "description": "Properly section and handle 'agent thinking' responses from the ai. Right now we just have <thinking> indicators not sure if thats a bodge or if there is a richer way we could be handling this..."
+}

conductor/tracks/thinking_trace_handling_20260313/plan.md

@@ -0,0 +1,23 @@
+# Implementation Plan: Rich Thinking Trace Handling
+
+## Status: COMPLETE (2026-03-14)
+
+## Summary
+Implemented thinking trace parsing, model, persistence, and GUI rendering for AI responses containing `<thinking>`, `<thought>`, and `Thinking:` markers.
+
+## 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
+
+## 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

conductor/tracks/thinking_trace_handling_20260313/spec.md

@@ -0,0 +1,31 @@
+# Specification: Rich Thinking Trace Handling
+
+## Overview
+Implement a formal system for parsing, storing, and rendering "agent thinking" monologues (chains of thought) within the Manual Slop GUI. Currently, thinking traces are treated as raw text or simple markers. This track will introduce a structured UI pattern to separate internal monologue from direct user responses while preserving both for future context.
+
+## Functional Requirements
+- **Multi-Format Parsing:** Support extraction of thinking traces from `<thinking>...</thinking>`, `<thought>...</thought>`, and blocks prefixed with `Thinking:`.
+- **Integrated UI Rendering:**
+  - In the **Comms History** and **Discussion Hub**, thinking traces must be rendered in a distinct, collapsible section.
+  - The section should be **Collapsed by Default** to minimize visual noise.
+  - Thinking traces must be visually separated from the "visible" response (e.g., using a tinted background, border, or specialized header).
+- **Persistent State Management:**
+  - Both the thinking monologue and the final response must be saved to the permanent discussion history (`manual_slop_history.toml` or `project_history.toml`).
+  - History entries must be properly tagged/schematized to distinguish between thinking and output.
+- **Context Recurrence:**
+  - Thinking traces must be included in subsequent AI turns (Full Recurrence) to maintain the model's internal state and logical progression.
+
+## Non-Functional Requirements
+- **Performance:** Parsing and rendering of thinking blocks must not introduce visible latency in the GUI thread.
+- **Accessibility:** All thinking blocks must remain selectable and copyable via the standard high-fidelity selectable UI pattern.
+
+## Acceptance Criteria
+- [ ] AI responses containing `<thinking>` or similar tags are automatically parsed into separate segments.
+- [ ] A "Thinking..." header appears in the Discussion Hub for messages with monologues.
+- [ ] Clicking the header expands the full thinking trace.
+- [ ] Saving/Loading a project preserves the distinction between thinking and response.
+- [ ] Subsequent AI calls receive the thinking trace as part of the conversation history.
+
+## Out of Scope
+- Implementing "Hidden Thinking" (where the user cannot see it but the AI can).
+- Real-time "Streaming" of thinking into the UI (unless already supported by the active provider).

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
@@ -31,14 +26,15 @@ separate_tier1 = false
 separate_tier2 = false
 separate_tier3 = false
 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
@@ -51,15 +47,18 @@ separate_tier4 = false
 "Operations Hub" = true
 Message = false
 Response = false
-"Tool Calls" = true
-Theme = true
-"Log Management" = true
+"Tool Calls" = false
+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/Inter-Regular.ttf"
-font_size = 14.0
+font_path = "fonts/Inter-Regular.ttf"
+font_size = 16.0
 scale = 1.0
 transparency = 1.0
 child_transparency = 1.0
@@ -69,3 +68,8 @@ max_workers = 4
 
 [headless]
 api_key = "test-secret-key"
+
+[paths]
+conductor_dir = "C:\\projects\\gencpp\\.ai\\conductor"
+logs_dir = "C:\\projects\\manual_slop\\logs"
+scripts_dir = "C:\\projects\\manual_slop\\scripts"

docs/guide_shaders_and_window.md

@@ -0,0 +1,33 @@
+# Custom Shaders and Window Frame Architecture
+
+## 1. Shader Injection Strategy
+
+### Evaluation
+*   **Dear PyGui (Legacy):** Does not natively support raw GLSL/HLSL shader injection into the UI layer. It relies heavily on fixed-function vertex/fragment shaders compiled into the C++ core. Faux-shaders via DrawList are the only viable path without modifying the DPG source.
+*   **imgui-bundle (Current):** `imgui-bundle` utilizes `hello_imgui` as its application runner, which provides robust lifecycle callbacks (e.g., `callbacks.custom_background`, `callbacks.post_init`). Because `hello_imgui` exposes the underlying OpenGL context, we can use `PyOpenGL` alongside it to execute raw GLSL shaders.
+
+### Chosen Approach: Hybrid Faux-Shader & PyOpenGL FBO
+Given the Python environment, we will adopt a hybrid approach:
+1.  **Faux-Shaders (ImDrawList Batching):** Continue using `imgui.ImDrawList` primitives for simple effects like soft shadows, glows, and basic gradients (as seen in `src/shaders.py`). This is highly performant for UI elements and requires no external dependencies.
+2.  **True GPU Shaders (PyOpenGL + FBO):** For complex post-processing (CRT curvature, bloom, dynamic noise backgrounds), we will integrate `PyOpenGL`. 
+    *   We will compile GLSL shaders during `post_init`.
+    *   We will render the effect into a Framebuffer Object (FBO).
+    *   We will display the resulting texture ID using `imgui.image()` or inject it into the `custom_background` callback.
+
+*Note: This approach introduces `PyOpenGL` as a dependency, which is standard for advanced Python graphics.*
+
+## 2. Custom Window Frame Strategy
+
+### Evaluation
+*   **Native DWM Overloading (PyWin32):** It is possible to use `pywin32` to subclass the application window, intercept `WM_NCHITTEST`, and return `HTCAPTION` for a custom ImGui-drawn title bar region. This preserves Windows snap layouts and native drop shadows. However, it is strictly Windows-only and can conflict with GLFW/SDL2 event loops used by `hello_imgui`.
+*   **Borderless Window Mode (ImGui/GLFW):** `hello_imgui` allows configuring the main window as borderless/undecorated (`runner_params.app_window_params.borderless = True`). We must then manually draw the title bar, minimize/maximize/close buttons, and handle window dragging by updating the OS window position based on ImGui mouse drag deltas.
+
+### Chosen Approach: Pure ImGui Borderless Implementation
+To ensure cross-platform compatibility and avoid brittle Win32 hook collisions with `hello_imgui`, we will use the **Borderless Window Mode** approach.
+1.  **Initialization:** Configure `hello_imgui.RunnerParams` to disable OS window decorations.
+2.  **Title Bar Rendering:** Dedicate the top ~30 pixels of the ImGui workspace to a custom title bar that matches the current theme (e.g., NERV or standard).
+3.  **Window Controls:** Implement custom ImGui buttons for `_`, `[]`, and `X`, which will call native window management functions exposed by `hello_imgui` or `glfw`.
+4.  **Drag Handling:** Detect `imgui.is_mouse_dragging()` on the title bar region and dynamically adjust the application window position.
+
+## 3. Integration with Event Metrics
+Both the shader uniforms (time, resolution) and window control events will be hooked into the existing `dag_engine` and `events` systems to ensure minimal performance overhead and centralized configuration via `config.toml`.

imgui.ini

@@ -0,0 +1,22 @@
+;;; !!! This configuration is handled by HelloImGui and stores several Ini Files, separated by markers like this:
+           ;;;<<<INI_NAME>>>;;;
+
+;;;<<<ImGui_655921752_Default>>>;;;
+[Window][Debug##Default]
+Pos=60,60
+Size=400,400
+Collapsed=0
+
+[Docking][Data]
+
+;;;<<<Layout_655921752_Default>>>;;;
+;;;<<<HelloImGui_Misc>>>;;;
+[Layout]
+Name=Default
+[StatusBar]
+Show=false
+ShowFps=true
+[Theme]
+Name=DarculaDarker
+;;;<<<SplitIds>>>;;;
+{"gImGuiSplitIDs":{}}

manual_slop_test.ini

@@ -0,0 +1,22 @@
+;;; !!! This configuration is handled by HelloImGui and stores several Ini Files, separated by markers like this:
+           ;;;<<<INI_NAME>>>;;;
+
+;;;<<<ImGui_655921752_Default>>>;;;
+[Window][Debug##Default]
+Pos=60,60
+Size=400,400
+Collapsed=0
+
+[Docking][Data]
+
+;;;<<<Layout_655921752_Default>>>;;;
+;;;<<<HelloImGui_Misc>>>;;;
+[Layout]
+Name=Default
+[StatusBar]
+Show=false
+ShowFps=true
+[Theme]
+Name=DarculaDarker
+;;;<<<SplitIds>>>;;;
+{"gImGuiSplitIDs":{}}

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=642,1879
-Size=1002,242
+Pos=711,694
+Size=716,455
 Collapsed=0
 
 [Window][Response]
-Pos=1700,1898
-Size=1111,224
+Pos=245,1014
+Size=1492,948
 Collapsed=0
 
 [Window][Tool Calls]
-Pos=790,1483
-Size=876,654
+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=0,1786
-Size=676,351
+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=2641,34
-Size=1199,2103
+Pos=1945,734
+Size=1211,713
 Collapsed=0
-DockId=0x00000010,2
 
 [Window][Context Hub]
-Pos=0,1786
-Size=676,351
+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=1668,22
-Size=915,2115
+Pos=1126,24
+Size=1638,1608
 Collapsed=0
-DockId=0x00000013,0
+DockId=0x00000006,0
 
 [Window][Operations Hub]
-Pos=678,22
-Size=988,2115
+Pos=0,24
+Size=1124,1608
 Collapsed=0
-DockId=0x00000005,0
+DockId=0x00000005,2
 
 [Window][Files & Media]
-Pos=0,1786
-Size=676,351
+Pos=1126,24
+Size=1638,1608
 Collapsed=0
-DockId=0x00000002,0
+DockId=0x00000006,1
 
 [Window][AI Settings]
-Pos=0,22
-Size=676,1762
+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=2585,22
-Size=1255,2115
+Pos=3360,26
+Size=480,2134
 Collapsed=0
-DockId=0x00000010,0
+DockId=0x00000004,0
 
 [Window][Log Management]
-Pos=2585,22
-Size=1255,2115
+Pos=3360,26
+Size=480,2134
 Collapsed=0
-DockId=0x00000010,1
+DockId=0x00000004,0
 
 [Window][Track Proposal]
 Pos=709,326
@@ -152,23 +151,20 @@ Collapsed=0
 Pos=2905,1238
 Size=935,899
 Collapsed=0
-DockId=0x00000004,0
 
 [Window][Tier 2: Tech Lead]
 Pos=2905,1238
 Size=935,899
 Collapsed=0
-DockId=0x00000004,0
 
 [Window][Tier 4: QA]
 Pos=2905,1238
 Size=935,899
 Collapsed=0
-DockId=0x00000004,0
 
 [Window][Tier 3: Workers]
-Pos=2641,1719
-Size=916,418
+Pos=2822,1717
+Size=1018,420
 Collapsed=0
 DockId=0x0000000C,0
 
@@ -178,8 +174,8 @@ Size=381,329
 Collapsed=0
 
 [Window][Last Script Output]
-Pos=1005,343
-Size=800,562
+Pos=1076,794
+Size=1085,1154
 Collapsed=0
 
 [Window][Text Viewer - Log Entry #1 (request)]
@@ -193,7 +189,7 @@ Size=1005,366
 Collapsed=0
 
 [Window][Text Viewer - Entry #11]
-Pos=60,60
+Pos=1010,564
 Size=1529,925
 Collapsed=0
 
@@ -223,13 +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]
@@ -243,8 +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]
@@ -288,8 +284,8 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - Tool Call #1 Details]
-Pos=2318,1220
-Size=900,700
+Pos=963,716
+Size=727,725
 Collapsed=0
 
 [Window][Text Viewer - Tool Call #10 Details]
@@ -333,8 +329,8 @@ Size=967,499
 Collapsed=0
 
 [Window][Usage Analytics]
-Pos=2641,1719
-Size=1199,418
+Pos=2678,26
+Size=1162,2134
 Collapsed=0
 DockId=0x0000000F,0
 
@@ -353,6 +349,68 @@ Pos=856,546
 Size=1000,800
 Collapsed=0
 
+[Window][External Tools]
+Pos=531,376
+Size=616,409
+Collapsed=0
+
+[Window][Text Viewer - Tool Call #2 Details]
+Pos=60,60
+Size=900,700
+Collapsed=0
+
+[Window][Text Viewer - Tool Call #3 Details]
+Pos=60,60
+Size=900,700
+Collapsed=0
+
+[Window][Text Viewer - Entry #4]
+Pos=1165,782
+Size=900,700
+Collapsed=0
+
+[Window][Text Viewer - Entry #10]
+Pos=755,715
+Size=1593,1240
+Collapsed=0
+
+[Window][Text Viewer - Entry #5]
+Pos=989,778
+Size=1366,1032
+Collapsed=0
+
+[Window][Shader Editor]
+Pos=457,710
+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
@@ -384,11 +442,11 @@ Column 3  Width=20
 Column 4  Weight=1.0000
 
 [Table][0x2A6000B6,4]
-RefScale=24
-Column 0  Width=72
-Column 1  Width=106
+RefScale=16
+Column 0  Width=48
+Column 1  Width=67
 Column 2  Weight=1.0000
-Column 3  Width=180
+Column 3  Width=243
 
 [Table][0x8BCC69C7,6]
 RefScale=13
@@ -400,18 +458,18 @@ Column 4  Weight=1.0000
 Column 5  Width=50
 
 [Table][0x3751446B,4]
-RefScale=14
-Column 0  Width=42
-Column 1  Width=63
+RefScale=18
+Column 0  Width=54
+Column 1  Width=81
 Column 2  Weight=1.0000
-Column 3  Width=105
+Column 3  Width=135
 
 [Table][0x2C515046,4]
-RefScale=24
-Column 0  Width=73
+RefScale=16
+Column 0  Width=48
 Column 1  Weight=1.0000
-Column 2  Width=181
-Column 3  Width=72
+Column 2  Width=166
+Column 3  Width=48
 
 [Table][0xD99F45C5,4]
 Column 0  Sort=0v
@@ -432,14 +490,14 @@ Column 1  Width=100
 Column 2  Weight=1.0000
 
 [Table][0xA02D8C87,3]
-RefScale=24
-Column 0  Width=270
-Column 1  Width=180
+RefScale=16
+Column 0  Width=179
+Column 1  Width=120
 Column 2  Weight=1.0000
 
 [Table][0xD0277E63,2]
-RefScale=14
-Column 0  Width=116
+RefScale=16
+Column 0  Width=132
 Column 1  Weight=1.0000
 
 [Table][0x3AAF84D5,2]
@@ -448,41 +506,35 @@ Column 0  Width=150
 Column 1  Weight=1.0000
 
 [Table][0x8D8494AB,2]
-RefScale=14
-Column 0  Width=116
+RefScale=18
+Column 0  Width=148
 Column 1  Weight=1.0000
 
 [Table][0x2C261E6E,2]
-RefScale=14
-Column 0  Width=87
+RefScale=18
+Column 0  Width=111
 Column 1  Weight=1.0000
 
 [Table][0x9CB1E6FD,2]
-RefScale=14
-Column 0  Width=164
+RefScale=16
+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=3840,2115 Split=X
-  DockNode          ID=0x00000003 Parent=0xAFC85805 SizeRef=2583,1183 Split=X
-    DockNode        ID=0x0000000B Parent=0x00000003 SizeRef=404,1186 Split=X Selected=0xF4139CA2
-      DockNode      ID=0x00000007 Parent=0x0000000B SizeRef=676,858 Split=Y Selected=0x8CA2375C
-        DockNode    ID=0x00000001 Parent=0x00000007 SizeRef=824,1759 CentralNode=1 Selected=0x7BD57D6A
-        DockNode    ID=0x00000002 Parent=0x00000007 SizeRef=824,351 Selected=0x1DCB2623
-      DockNode      ID=0x0000000E Parent=0x0000000B SizeRef=1905,858 Split=X Selected=0x418C7449
-        DockNode    ID=0x00000012 Parent=0x0000000E SizeRef=988,402 Split=Y Selected=0x418C7449
-          DockNode  ID=0x00000005 Parent=0x00000012 SizeRef=876,1455 Selected=0x418C7449
-          DockNode  ID=0x00000006 Parent=0x00000012 SizeRef=876,654 Selected=0x1D56B311
-        DockNode    ID=0x00000013 Parent=0x0000000E SizeRef=915,402 Selected=0x6F2B5B04
-    DockNode        ID=0x0000000D Parent=0x00000003 SizeRef=435,1186 Selected=0x363E93D6
-  DockNode          ID=0x00000004 Parent=0xAFC85805 SizeRef=1255,1183 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"]
 }

presets.toml

@@ -1,2 +1,5 @@
 [presets.Default]
 system_prompt = ""
+
+[presets.ModalPreset]
+system_prompt = "Modal Content"

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 = "2026-03-10T21:01:58"
+last_updated = "2026-03-22T12:59:02"
 history = []

pyproject.toml

@@ -17,6 +17,7 @@ dependencies = [
     "tree-sitter-python>=0.25.0",
     "mcp>=1.0.0",
     "pytest-timeout>=2.4.0",
+    "pyopengl>=3.1.10",
 ]
 
 [dependency-groups]

scripts/mock_mcp_server.py

@@ -0,0 +1,47 @@
+import sys
+import json
+
+def main():
+    while True:
+        line = sys.stdin.readline()
+        if not line:
+            break
+        try:
+            req = json.loads(line)
+            method = req.get("method")
+            req_id = req.get("id")
+            
+            if method == "tools/list":
+                resp = {
+                    "jsonrpc": "2.0",
+                    "id": req_id,
+                    "result": {
+                        "tools": [
+                            {"name": "echo", "description": "Echo input", "inputSchema": {"type": "object"}}
+                        ]
+                    }
+                }
+            elif method == "tools/call":
+                name = req["params"].get("name")
+                args = req["params"].get("arguments", {})
+                if name == "echo":
+                    resp = {
+                        "jsonrpc": "2.0",
+                        "id": req_id,
+                        "result": {
+                            "content": [{"type": "text", "text": f"ECHO: {args}"}]
+                        }
+                    }
+                else:
+                    resp = {"jsonrpc": "2.0", "id": req_id, "error": {"message": "Unknown tool"}}
+            else:
+                resp = {"jsonrpc": "2.0", "id": req_id, "error": {"message": "Unknown method"}}
+            
+            sys.stdout.write(json.dumps(resp) + "\n")
+            sys.stdout.flush()
+        except Exception as e:
+            sys.stderr.write(f"Error: {e}\n")
+            sys.stderr.flush()
+
+if __name__ == "__main__":
+    main()

scripts/temp_handle_test.py

@@ -0,0 +1,12 @@
+from imgui_bundle import hello_imgui, imgui
+
+def on_gui():
+    imgui.text("Hello world")
+
+params = hello_imgui.RunnerParams()
+params.app_window_params.borderless = True
+params.app_window_params.borderless_movable = True
+params.app_window_params.borderless_resizable = True
+params.app_window_params.borderless_closable = True
+
+hello_imgui.run(params)

src/ai_client.py

@@ -535,7 +535,7 @@ def get_bias_profile() -> Optional[str]:
 
 def _build_anthropic_tools() -> list[dict[str, Any]]:
  raw_tools: list[dict[str, Any]] = []
- for spec in mcp_client.MCP_TOOL_SPECS:
+ for spec in mcp_client.get_tool_schemas():
   if _agent_tools.get(spec["name"], True):
    raw_tools.append({
      "name": spec["name"],
@@ -579,7 +579,7 @@ def _get_anthropic_tools() -> list[dict[str, Any]]:
 
 def _gemini_tool_declaration() -> Optional[types.Tool]:
  raw_tools: list[dict[str, Any]] = []
- for spec in mcp_client.MCP_TOOL_SPECS:
+ for spec in mcp_client.get_tool_schemas():
   if _agent_tools.get(spec["name"], True):
    raw_tools.append({
     "name": spec["name"],
@@ -715,10 +715,15 @@ async def _execute_single_tool_call_async(
    tool_executed = True
 
  if not tool_executed:
-  if name and name in mcp_client.TOOL_NAMES:
+  is_native = name in mcp_client.TOOL_NAMES
+  ext_tools = mcp_client.get_external_mcp_manager().get_all_tools()
+  is_external = name in ext_tools
+  if name and (is_native or is_external):
    _append_comms("OUT", "tool_call", {"name": name, "id": call_id, "args": args})
-   if name in mcp_client.MUTATING_TOOLS and approval_mode != "auto" and pre_tool_callback:
-    desc = f"# MCP MUTATING TOOL: {name}\n" + "\n".join(f"#   {k}: {repr(v)}" for k, v in args.items())
+   should_approve = (name in mcp_client.MUTATING_TOOLS or is_external) and approval_mode != "auto" and pre_tool_callback
+   if should_approve:
+    label = "MCP MUTATING" if is_native else "EXTERNAL MCP"
+    desc = f"# {label} TOOL: {name}\n" + "\n".join(f"#   {k}: {repr(v)}" for k, v in args.items())
     _res = await asyncio.to_thread(pre_tool_callback, desc, base_dir, qa_callback)
     out = "USER REJECTED: tool execution cancelled" if _res is None else await mcp_client.async_dispatch(name, args)
    else:
@@ -816,7 +821,7 @@ def _build_file_diff_text(changed_items: list[dict[str, Any]]) -> str:
 
 def _build_deepseek_tools() -> list[dict[str, Any]]:
  raw_tools: list[dict[str, Any]] = []
- for spec in mcp_client.MCP_TOOL_SPECS:
+ for spec in mcp_client.get_tool_schemas():
   if _agent_tools.get(spec["name"], True):
    raw_tools.append({
     "name": spec["name"],

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")
@@ -643,7 +646,7 @@ class HookServer:
   if not _has_app_attr(self.app, '_api_event_queue'): _set_app_attr(self.app, '_api_event_queue', [])
   if not _has_app_attr(self.app, '_api_event_queue_lock'): _set_app_attr(self.app, '_api_event_queue_lock', threading.Lock())
   
-  self.websocket_server = WebSocketServer(self.app)
+  self.websocket_server = WebSocketServer(self.app, port=self.port + 1)
   self.websocket_server.start()
   
   eq = _get_app_attr(self.app, 'event_queue')

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
@@ -154,6 +155,7 @@ class AppController:
   self._loop_thread: Optional[threading.Thread] = None
   self.tracks: List[Dict[str, Any]] = []
   self.active_track: Optional[models.Track] = None
+  self.engine: Optional[multi_agent_conductor.ConductorEngine] = None
   self.active_tickets: List[Dict[str, Any]] = []
   self.mma_streams: Dict[str, str] = {}
   self._worker_status: Dict[str, str] = {}  # stream_id -> "running" | "completed" | "failed" | "killed"
@@ -179,7 +181,8 @@ class AppController:
    "cache_read_input_tokens": 0,
    "cache_creation_input_tokens": 0,
    "total_tokens": 0,
-   "last_latency": 0.0
+   "last_latency": 0.0,
+   "percentage": 0.0
   }
   self.mma_tier_usage: Dict[str, Dict[str, Any]] = {
    "Tier 1": {"input": 0, "output": 0, "provider": "gemini", "model": "gemini-3.1-pro-preview", "tool_preset": None},
@@ -196,6 +199,7 @@ class AppController:
   self._pending_dialog_open: bool = False
   self._pending_actions: Dict[str, ConfirmDialog] = {}
   self._pending_ask_dialog: bool = False
+  self.mcp_config: models.MCPConfiguration = models.MCPConfiguration()
   # AI settings state
   self._current_provider: str = "gemini"
   self._current_model: str = "gemini-2.5-flash-lite"
@@ -226,7 +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 = ""
@@ -239,6 +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
@@ -248,6 +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]] = []
@@ -283,7 +289,9 @@ class AppController:
   self._gemini_cache_text: str = ""
   self._last_stable_md: str = ''
   self._token_stats: Dict[str, Any] = {}
-  self._token_stats_dirty: bool = False
+  self._comms_log_dirty: bool = True
+  self._tool_log_dirty: bool = True
+  self._token_stats_dirty: bool = True
   self.ui_disc_truncate_pairs: int = 2
   self.ui_auto_scroll_comms: bool = True
   self.ui_auto_scroll_tool_calls: bool = True
@@ -291,10 +299,14 @@ class AppController:
   self._track_discussion_active: bool = False
   self._tier_stream_last_len: Dict[str, int] = {}
   self.is_viewing_prior_session: bool = False
+  self._current_session_usage = None
+  self._current_mma_tier_usage = None
   self.prior_session_entries: List[Dict[str, Any]] = []
   self.prior_tool_calls: List[Dict[str, Any]] = []
   self.prior_disc_entries: List[Dict[str, Any]] = []
-  self.prior_mma_dashboard_state: Dict[str, Any] = {}
+  self.prior_mma_dashboard_state = {}
+  self._current_token_history = None
+  self._current_session_start_time = None
   self.test_hooks_enabled: bool = ("--enable-test-hooks" in sys.argv) or (os.environ.get("SLOP_TEST_HOOKS") == "1")
   self.ui_manual_approve: bool = False
   # Injection state
@@ -365,7 +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({
@@ -412,7 +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
@@ -428,6 +446,12 @@ class AppController:
   if hasattr(self, 'perf_monitor'):
    self.perf_monitor.enabled = value
 
+ @property
+ def active_project_root(self) -> str:
+  if self.active_project_path:
+   return str(Path(self.active_project_path).parent)
+  return self.ui_files_base_dir
+
  def _update_inject_preview(self) -> None:
   """Updates the preview content based on the selected file and injection mode."""
   if not self._inject_file_path:
@@ -435,7 +459,7 @@ class AppController:
    return
   target_path = self._inject_file_path
   if not os.path.isabs(target_path):
-   target_path = os.path.join(self.ui_files_base_dir, target_path)
+   target_path = os.path.join(self.active_project_root, target_path)
   if not os.path.exists(target_path):
    self._inject_preview = ""
    return
@@ -522,6 +546,11 @@ class AppController:
      "payload": status
     })
 
+ def _trigger_gui_refresh(self):
+  with self._pending_gui_tasks_lock:
+   self._pending_gui_tasks.append({'action': 'set_comms_dirty'})
+   self._pending_gui_tasks.append({'action': 'set_tool_log_dirty'})
+
  def _process_pending_gui_tasks(self) -> None:
   # Periodic telemetry broadcast
   now = time.time()
@@ -548,6 +577,10 @@ class AppController:
      # ...
     if action == "refresh_api_metrics":
      self._refresh_api_metrics(task.get("payload", {}), md_content=self.last_md or None)
+    elif action == 'set_comms_dirty':
+     self._comms_log_dirty = True
+    elif action == 'set_tool_log_dirty':
+     self._tool_log_dirty = True
     elif action == "set_ai_status":
      self.ai_status = task.get("payload", "")
      sys.stderr.write(f"[DEBUG] Updated ai_status via task to: {self.ai_status}\n")
@@ -586,16 +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")
@@ -842,7 +865,11 @@ class AppController:
   self.ui_separate_tier2 = False
   self.ui_separate_tier3 = False
   self.ui_separate_tier4 = False
+  self.ui_separate_external_tools = False
   self.config = models.load_config()
+  path_info = paths.get_full_path_info()
+  self.ui_logs_dir = str(path_info['logs_dir']['path'])
+  self.ui_scripts_dir = str(path_info['scripts_dir']['path'])
   theme.load_from_config(self.config)
   ai_cfg = self.config.get("ai", {})
   self._current_provider = ai_cfg.get("provider", "gemini")
@@ -878,12 +905,12 @@ class AppController:
   self.ui_shots_base_dir = self.project.get("screenshots", {}).get("base_dir", ".")
   proj_meta = self.project.get("project", {})
   self.ui_project_git_dir = proj_meta.get("git_dir", "")
+  self.ui_project_conductor_dir = self.project.get('conductor', {}).get('dir', 'conductor')
   self.ui_project_main_context = proj_meta.get("main_context", "")
   self.ui_project_system_prompt = proj_meta.get("system_prompt", "")
   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", "")
   
@@ -893,6 +920,18 @@ class AppController:
   self.tool_presets = self.tool_preset_manager.load_all_presets()
   self.bias_profiles = self.tool_preset_manager.load_all_bias_profiles()
 
+  mcp_path = self.project.get('project', {}).get('mcp_config_path') or self.config.get('ai', {}).get('mcp_config_path')
+  if mcp_path:
+   mcp_p = Path(mcp_path)
+   if not mcp_p.is_absolute() and self.active_project_path:
+    mcp_p = Path(self.active_project_path).parent / mcp_path
+   if mcp_p.exists():
+    self.mcp_config = models.load_mcp_config(str(mcp_p))
+   else:
+    self.mcp_config = models.MCPConfiguration()
+  else:
+   self.mcp_config = models.MCPConfiguration()
+
   from src.personas import PersonaManager
   self.persona_manager = PersonaManager(Path(self.active_project_path).parent if self.active_project_path else None)
   self.personas = self.persona_manager.load_all()
@@ -911,7 +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,
@@ -938,7 +977,16 @@ class AppController:
   agent_tools_cfg = self.project.get("agent", {}).get("tools", {})
   self.ui_agent_tools = {t: agent_tools_cfg.get(t, True) for t in models.AGENT_TOOL_NAMES}
   label = self.project.get("project", {}).get("name", "")
-  session_logger.open_session(label=label)
+  session_logger.reset_session(label=label)
+  # Trigger auto-start of MCP servers
+  self.event_queue.put('refresh_external_mcps', None)
+
+ async def refresh_external_mcps(self):
+  await mcp_client.get_external_mcp_manager().stop_all()
+  # Start servers with auto_start=True
+  for name, cfg in self.mcp_config.mcpServers.items():
+   if cfg.auto_start:
+    await mcp_client.get_external_mcp_manager().add_server(cfg)
 
  def cb_load_prior_log(self, path: Optional[str] = None) -> None:
   root = hide_tk_root()
@@ -951,6 +999,12 @@ class AppController:
   if not path:
    return
   
+  if not self.is_viewing_prior_session:
+   self._current_session_usage = copy.deepcopy(self.session_usage)
+   self._current_mma_tier_usage = copy.deepcopy(self.mma_tier_usage)
+   self._current_token_history = copy.deepcopy(self._token_history)
+   self._current_session_start_time = self._session_start_time
+
   log_path = Path(path)
   if log_path.is_dir():
    log_file = log_path / "comms.log"
@@ -985,6 +1039,15 @@ class AppController:
 
   entries = []
   disc_entries = []
+  paired_tools = {}
+  final_tool_calls = []
+  new_token_history = []
+  new_usage = {'input_tokens': 0, 'output_tokens': 0, 'cache_read_input_tokens': 0, 'cache_creation_input_tokens': 0, 'total_tokens': 0, 'last_latency': 0.0, 'percentage': 0.0}
+  new_mma_usage = copy.deepcopy(self.mma_tier_usage)
+  for t in new_mma_usage:
+   new_mma_usage[t]['input'] = 0
+   new_mma_usage[t]['output'] = 0
+
   try:
    with open(log_file, "r", encoding="utf-8") as f:
     for line in f:
@@ -997,6 +1060,47 @@ class AppController:
        payload = entry.get("payload", {})
        ts = entry.get("ts", "")
 
+       if kind == 'tool_call':
+        tid = payload.get('id') or payload.get('call_id')
+        script = payload.get('script') or json.dumps(payload.get('args', {}), indent=1)
+        script = _resolve_log_ref(script, session_dir)
+        entry_obj = {
+         'source_tier': entry.get('source_tier', 'main'),
+         'script': script,
+         'result': '', # Waiting for result
+         'ts': ts
+        }
+        if tid:
+         paired_tools[tid] = entry_obj
+        final_tool_calls.append(entry_obj)
+       elif kind == 'tool_result':
+        tid = payload.get('id') or payload.get('call_id')
+        output = payload.get('output', payload.get('content', ''))
+        output = _resolve_log_ref(output, session_dir)
+        if tid and tid in paired_tools:
+         paired_tools[tid]['result'] = output
+        else:
+         # Fallback: if no ID, try matching last entry in final_tool_calls that has no result
+         for old_call in reversed(final_tool_calls):
+          if not old_call['result']:
+           old_call['result'] = output
+           break
+
+       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 new_usage: new_usage[k] += u.get(k, 0) or 0
+        tier = entry.get('source_tier', 'main')
+        if tier in new_mma_usage:
+         new_mma_usage[tier]['input'] += u.get('input_tokens', 0) or 0
+         new_mma_usage[tier]['output'] += u.get('output_tokens', 0) or 0
+        new_token_history.append({
+         'time': ts,
+         'input': u.get('input_tokens', 0) or 0,
+         'output': u.get('output_tokens', 0) or 0,
+         'model': entry.get('model', 'unknown')
+        })
+       
        if kind == "history_add":
         content = payload.get("content", payload.get("text", payload.get("message", "")))
         content = _resolve_log_ref(content, session_dir)
@@ -1053,11 +1157,47 @@ class AppController:
    self._set_status(f"log load error: {e}")
    return
   
+  self.session_usage = new_usage
+  self.mma_tier_usage = new_mma_usage
+  self._token_history = new_token_history
+  if new_token_history:
+   try:
+    import datetime
+    first_ts = new_token_history[0]['time']
+    dt = datetime.datetime.strptime(first_ts, '%Y-%m-%dT%H:%M:%S')
+    self._session_start_time = dt.timestamp()
+   except:
+    self._session_start_time = time.time()
   self.prior_session_entries = entries
   self.prior_disc_entries = disc_entries
+  self.prior_tool_calls = final_tool_calls
   self.is_viewing_prior_session = True
+  self._trigger_gui_refresh()
   self._set_status(f"viewing prior session: {session_dir.name} ({len(entries)} entries)")
 
+
+ def cb_exit_prior_session(self):
+  self.is_viewing_prior_session = False
+  if self._current_session_usage:
+   self.session_usage = self._current_session_usage
+   self._current_session_usage = None
+  if self._current_mma_tier_usage:
+   self.mma_tier_usage = self._current_mma_tier_usage
+   self._current_mma_tier_usage = None
+
+  if self._current_token_history is not None:
+   self._token_history = self._current_token_history
+   self._current_token_history = None
+  if self._current_session_start_time is not None:
+   self._session_start_time = self._current_session_start_time
+   self._current_session_start_time = None
+
+  self.prior_session_entries.clear()
+  self.prior_disc_entries.clear()
+  self.prior_tool_calls.clear()
+  self._trigger_gui_refresh()
+  self._set_status('idle')
+
  def cb_prune_logs(self) -> None:
   """Manually triggers the log pruning process with aggressive thresholds."""
   self._set_status("Manual prune started (Age > 0d, Size < 100KB)...")
@@ -1252,9 +1392,13 @@ class AppController:
        "action": "ticket_completed",
        "payload": payload
       })
+   elif event_name == "refresh_external_mcps":
+    import asyncio
+    asyncio.run(self.refresh_external_mcps())
 
  def _handle_request_event(self, event: events.UserRequestEvent) -> None:
   """Processes a UserRequestEvent by calling the AI client."""
+  self._set_status('sending...')
   ai_client.set_current_tier(None) # Ensure main discussion is untagged
   # Clear response area for new turn
   self.ai_response = ""
@@ -1321,9 +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")
@@ -1344,22 +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:
@@ -1643,7 +1820,7 @@ class AppController:
     except Exception as e:
      raise HTTPException(status_code=500, detail=f"Context aggregation failure: {e}")
     user_msg = req.prompt
-    base_dir = self.ui_files_base_dir
+    base_dir = self.active_project_root
     csp = filter(bool, [self.ui_global_system_prompt.strip(), self.ui_project_system_prompt.strip()])
     ai_client.set_custom_system_prompt("\n\n".join(csp))
     temp = req.temperature if req.temperature is not None else self.temperature
@@ -1751,7 +1928,7 @@ class AppController:
     return {
      "files": [f.get("path") if isinstance(f, dict) else str(f) for f in file_items],
      "screenshots": screenshots,
-     "files_base_dir": self.ui_files_base_dir,
+     "files_base_dir": self.active_project_root,
      "markdown": md,
      "discussion": disc_text
     }
@@ -1775,7 +1952,6 @@ class AppController:
 
  def _cb_project_save(self) -> None:
   self._flush_to_project()
-  self._save_active_project()
   self._flush_to_config()
   models.save_config(self.config)
   self._set_status("config saved")
@@ -1791,10 +1967,14 @@ class AppController:
    self._set_status(f"project file not found: {path}")
    return
   self._flush_to_project()
-  self._save_active_project()
   try:
    self.project = project_manager.load_project(path)
    self.active_project_path = path
+   new_root = Path(path).parent
+   self.preset_manager = presets.PresetManager(new_root)
+   self.tool_preset_manager = tool_presets.ToolPresetManager(new_root)
+   from src.personas import PersonaManager
+   self.persona_manager = PersonaManager(new_root)
   except Exception as e:
    self._set_status(f"failed to load project: {e}")
    return
@@ -1824,11 +2004,10 @@ 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
-  self.tracks = project_manager.get_all_tracks(self.ui_files_base_dir)
+  self.tracks = project_manager.get_all_tracks(self.active_project_root)
   # Restore MMA state
   mma_sec = proj.get("mma", {})
   self.ui_epic_input = mma_sec.get("epic", "")
@@ -1858,18 +2037,19 @@ class AppController:
    self.active_tickets = []
    # Load track-scoped history if track is active
   if self.active_track:
-   track_history = project_manager.load_track_history(self.active_track.id, self.ui_files_base_dir)
+   track_history = project_manager.load_track_history(self.active_track.id, self.active_project_root)
    if track_history:
     with self._disc_entries_lock:
      self.disc_entries = models.parse_history_entries(track_history, self.disc_roles)
   
-  self.preset_manager.project_root = Path(self.ui_files_base_dir)
+  self.preset_manager.project_root = Path(self.active_project_root)
   self.presets = self.preset_manager.load_all()
-  self.tool_preset_manager.project_root = Path(self.ui_files_base_dir)
+  self.tool_preset_manager.project_root = Path(self.active_project_root)
   self.tool_presets = self.tool_preset_manager.load_all_presets()
   self.bias_profiles = self.tool_preset_manager.load_all_bias_profiles()
 
  def _apply_preset(self, name: str, scope: str) -> None:
+  print(f"[DEBUG] _apply_preset: name={name}, scope={scope}")
   if name == "None":
    if scope == "global":
     self.ui_global_preset_name = ""
@@ -1878,6 +2058,7 @@ class AppController:
    return
   preset = self.presets.get(name)
   if not preset:
+   print(f"[DEBUG] _apply_preset: preset {name} not found in {list(self.presets.keys())}")
    return
   if scope == "global":
    self.ui_global_system_prompt = preset.system_prompt
@@ -1887,6 +2068,7 @@ class AppController:
    self.ui_project_preset_name = name
 
  def _cb_save_preset(self, name, content, scope):
+  print(f"[DEBUG] _cb_save_preset: name={name}, scope={scope}")
   if not name or not name.strip():
    raise ValueError("Preset name cannot be empty or whitespace.")
   preset = models.Preset(
@@ -1895,6 +2077,7 @@ class AppController:
   )
   self.preset_manager.save_preset(preset, scope)
   self.presets = self.preset_manager.load_all()
+  print(f"[DEBUG] _cb_save_preset: saved {name}, total presets now {len(self.presets)}")
 
  def _cb_delete_preset(self, name, scope):
   self.preset_manager.delete_preset(name, scope)
@@ -1927,7 +2110,7 @@ class AppController:
 
 
  def _cb_load_track(self, track_id: str) -> None:
-  state = project_manager.load_track_state(track_id, self.ui_files_base_dir)
+  state = project_manager.load_track_state(track_id, self.active_project_root)
   if state:
    try:
    # Convert list[Ticket] or list[dict] to list[Ticket] for Track object
@@ -1945,7 +2128,7 @@ class AppController:
     # Keep dicts for UI table (or convert models.Ticket objects back to dicts if needed)
     self.active_tickets = [asdict(t) if not isinstance(t, dict) else t for t in tickets]
     # Load track-scoped history
-    history = project_manager.load_track_history(track_id, self.ui_files_base_dir)
+    history = project_manager.load_track_history(track_id, self.active_project_root)
     with self._disc_entries_lock:
      if history:
       self.disc_entries = models.parse_history_entries(history, self.disc_roles)
@@ -1960,7 +2143,8 @@ class AppController:
  def _save_active_project(self) -> None:
   if self.active_project_path:
    try:
-    project_manager.save_project(self.project, self.active_project_path)
+    cleaned = project_manager.clean_nones(self.project)
+    project_manager.save_project(cleaned, self.active_project_path)
    except Exception as e:
     self._set_status(f"save error: {e}")
 
@@ -1987,7 +2171,7 @@ class AppController:
  def _flush_disc_entries_to_project(self) -> None:
   history_strings = [project_manager.entry_to_str(e) for e in self.disc_entries]
   if self.active_track and self._track_discussion_active:
-   project_manager.save_track_history(self.active_track.id, history_strings, self.ui_files_base_dir)
+   project_manager.save_track_history(self.active_track.id, history_strings, self.active_project_root)
    return
   disc_sec = self.project.setdefault("discussion", {})
   discussions = disc_sec.setdefault("discussions", {})
@@ -2004,6 +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", {})
@@ -2157,7 +2355,7 @@ class AppController:
       file_path, definition, line = res
       user_msg += f'\n\n[Definition: {symbol} from {file_path} (line {line})]\n```python\n{definition}\n```'
 
-    base_dir = self.ui_files_base_dir
+    base_dir = self.active_project_root
     sys.stderr.write(f"[DEBUG] _do_generate success. Prompt: {user_msg[:50]}...\n")
     sys.stderr.flush()
     # Prepare event payload
@@ -2180,7 +2378,7 @@ class AppController:
   threading.Thread(target=worker, daemon=True).start()
 
  def _recalculate_session_usage(self) -> None:
-  usage = {"input_tokens": 0, "output_tokens": 0, "cache_read_input_tokens": 0, "cache_creation_input_tokens": 0, "total_tokens": 0, "last_latency": 0.0}
+  usage = {"input_tokens": 0, "output_tokens": 0, "cache_read_input_tokens": 0, "cache_creation_input_tokens": 0, "total_tokens": 0, "last_latency": 0.0, "percentage": self.session_usage.get("percentage", 0.0)}
   for entry in ai_client.get_comms_log():
    if entry.get("kind") == "response" and "usage" in entry.get("payload", {}):
     u = entry["payload"]["usage"]
@@ -2195,6 +2393,8 @@ class AppController:
  def _refresh_api_metrics(self, payload: dict[str, Any], md_content: str | None = None) -> None:
   if "latency" in payload:
    self.session_usage["last_latency"] = payload["latency"]
+  if "usage" in payload and "percentage" in payload["usage"]:
+   self.session_usage["percentage"] = payload["usage"]["percentage"]
   self._recalculate_session_usage()
   if md_content is not None:
    stats = ai_client.get_token_stats(md_content)
@@ -2250,11 +2450,11 @@ class AppController:
   proj["screenshots"]["paths"] = self.screenshots
   proj.setdefault("project", {})
   proj["project"]["git_dir"] = self.ui_project_git_dir
+  proj.setdefault("conductor", {})["dir"] = self.ui_project_conductor_dir
   proj["project"]["system_prompt"] = self.ui_project_system_prompt
   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
@@ -2275,6 +2475,9 @@ class AppController:
   else:
    mma_sec["active_track"] = None
 
+  cleaned_proj = project_manager.clean_nones(proj)
+  project_manager.save_project(cleaned_proj, self.active_project_path)
+
  def _flush_to_config(self) -> None:
   self.config["ai"] = {
    "provider": self.current_provider,
@@ -2295,6 +2498,7 @@ class AppController:
    "separate_message_panel": getattr(self, "ui_separate_message_panel", False),
    "separate_response_panel": getattr(self, "ui_separate_response_panel", False),
    "separate_tool_calls_panel": getattr(self, "ui_separate_tool_calls_panel", False),
+   "separate_external_tools": getattr(self, "ui_separate_external_tools", False),
    "separate_task_dag": self.ui_separate_task_dag,
    "separate_usage_analytics": self.ui_separate_usage_analytics,
    "separate_tier1": self.ui_separate_tier1,
@@ -2311,7 +2515,6 @@ class AppController:
  def _do_generate(self) -> tuple[str, Path, list[dict[str, Any]], str, str]:
   """Returns (full_md, output_path, file_items, stable_md, discussion_text)."""
   self._flush_to_project()
-  self._save_active_project()
   self._flush_to_config()
   models.save_config(self.config)
   track_id = self.active_track.id if self.active_track else None
@@ -2325,6 +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:
@@ -2338,7 +2546,7 @@ class AppController:
     sys.stderr.flush()
     proj = project_manager.load_project(self.active_project_path)
     flat = project_manager.flat_config(self.project)
-    file_items = aggregate.build_file_items(Path(self.ui_files_base_dir), flat.get("files", {}).get("paths", []))
+    file_items = aggregate.build_file_items(Path(self.active_project_root), flat.get("files", {}).get("paths", []))
 
     _t1_baseline = len(ai_client.get_comms_log())
     tracks = orchestrator_pm.generate_tracks(self.ui_epic_input, flat, file_items, history_summary=history)
@@ -2390,7 +2598,7 @@ class AppController:
     for i, file_path in enumerate(files_to_scan):
      try:
       self._set_status(f"Phase 2: Scanning files ({i+1}/{len(files_to_scan)})...")
-      abs_path = Path(self.ui_files_base_dir) / file_path
+      abs_path = Path(self.active_project_root) / file_path
       if abs_path.exists() and abs_path.suffix == ".py":
        with open(abs_path, "r", encoding="utf-8") as f:
         code = f.read()
@@ -2425,6 +2633,7 @@ class AppController:
    # Use the active track object directly to start execution
     self._set_mma_status("running")
     engine = multi_agent_conductor.ConductorEngine(self.active_track, self.event_queue, auto_queue=not self.mma_step_mode)
+    self.engine = engine
     flat = project_manager.flat_config(self.project, self.active_discussion, track_id=self.active_track.id)
     full_md, _, _ = aggregate.run(flat)
     threading.Thread(target=engine.run, kwargs={"md_content": full_md}, daemon=True).start()
@@ -2491,13 +2700,14 @@ class AppController:
    # Initialize track state in the filesystem
    meta = models.Metadata(id=track_id, name=title, status="todo", created_at=datetime.now(), updated_at=datetime.now())
    state = models.TrackState(metadata=meta, discussion=[], tasks=tickets)
-   project_manager.save_track_state(track_id, state, self.ui_files_base_dir)
+   project_manager.save_track_state(track_id, state, self.active_project_root)
    # Add to memory and notify UI
    self.tracks.append({"id": track_id, "title": title, "status": "todo"})
    with self._pending_gui_tasks_lock:
     self._pending_gui_tasks.append({'action': 'refresh_from_project'})
     # 4. Initialize ConductorEngine and run loop
    engine = multi_agent_conductor.ConductorEngine(track, self.event_queue, auto_queue=not self.mma_step_mode)
+   self.engine = engine
    # Use current full markdown context for the track execution
    track_id_param = track.id
    flat = project_manager.flat_config(self.project, self.active_discussion, track_id=track_id_param)
@@ -2522,8 +2732,68 @@ class AppController:
     break
   self.event_queue.put("mma_skip", {"ticket_id": ticket_id})
 
+ def _spawn_worker(self, ticket_id: str, data: dict = None) -> None:
+  """Manually initiates a sub-agent execution for a ticket."""
+  if self.engine:
+   for t in self.active_track.tickets:
+    if t.id == ticket_id:
+     t.status = "todo"
+     t.step_mode = False
+     break
+   self.engine.engine.auto_queue = True
+  self.event_queue.put("mma_retry", {"ticket_id": ticket_id})
+
+ def kill_worker(self, worker_id: str) -> None:
+  """Aborts a running worker."""
+  if self.engine:
+   self.engine.kill_worker(worker_id)
+
+ def pause_mma(self) -> None:
+  """Pauses the global MMA loop."""
+  self.mma_step_mode = True
+  if self.engine:
+   self.engine.pause()
+
+ def resume_mma(self) -> None:
+  """Resumes the global MMA loop."""
+  self.mma_step_mode = False
+  if self.engine:
+   self.engine.resume()
+
+ def inject_context(self, data: dict) -> None:
+  """Programmatic context injection."""
+  file_path = data.get("file_path")
+  if file_path:
+   if not os.path.isabs(file_path):
+    file_path = os.path.relpath(file_path, self.active_project_root)
+   existing = next((f for f in self.files if (f.path if hasattr(f, "path") else str(f)) == file_path), None)
+   if not existing:
+    item = models.FileItem(path=file_path)
+    self.files.append(item)
+    self._refresh_from_project()
+
+ def mutate_dag(self, data: dict) -> None:
+  """Modifies task dependencies."""
+  ticket_id = data.get("ticket_id")
+  depends_on = data.get("depends_on")
+  if ticket_id and depends_on is not None:
+   for t in self.active_tickets:
+    if t.get("id") == ticket_id:
+     t["depends_on"] = depends_on
+     break
+   if self.active_track:
+    for t in self.active_track.tickets:
+     if t.id == ticket_id:
+      t.depends_on = depends_on
+      break
+    if self.engine:
+     from src.dag_engine import TrackDAG, ExecutionEngine
+     self.engine.dag = TrackDAG(self.active_track.tickets)
+     self.engine.engine = ExecutionEngine(self.engine.dag, auto_queue=self.engine.engine.auto_queue)
+   self._push_mma_state_update()
+
  def _cb_run_conductor_setup(self) -> None:
-  base = paths.get_conductor_dir()
+  base = paths.get_conductor_dir(project_path=self.active_project_root)
   if not base.exists():
    self.ui_conductor_setup_summary = f"Error: {base}/ directory not found."
    return
@@ -2553,7 +2823,7 @@ class AppController:
   if not name: return
   date_suffix = datetime.now().strftime("%Y%m%d")
   track_id = f"{name.lower().replace(' ', '_')}_{date_suffix}"
-  track_dir = paths.get_tracks_dir() / track_id
+  track_dir = paths.get_track_state_dir(track_id, project_path=self.active_project_root)
   track_dir.mkdir(parents=True, exist_ok=True)
   spec_file = track_dir / "spec.md"
   with open(spec_file, "w", encoding="utf-8") as f:
@@ -2572,7 +2842,7 @@ class AppController:
      "progress": 0.0
     }, f, indent=1)
    # Refresh tracks from disk
-  self.tracks = project_manager.get_all_tracks(self.ui_files_base_dir)
+  self.tracks = project_manager.get_all_tracks(self.active_project_root)
 
  def _push_mma_state_update(self) -> None:
   if not self.active_track:
@@ -2580,7 +2850,7 @@ class AppController:
    # Sync active_tickets (list of dicts) back to active_track.tickets (list of models.Ticket objects)
   self.active_track.tickets = [models.Ticket.from_dict(t) for t in self.active_tickets]
   # Save the state to disk
-  existing = project_manager.load_track_state(self.active_track.id, self.ui_files_base_dir)
+  existing = project_manager.load_track_state(self.active_track.id, self.active_project_root)
   meta = models.Metadata(
    id=self.active_track.id,
    name=self.active_track.description,
@@ -2593,5 +2863,5 @@ class AppController:
    discussion=existing.discussion if existing else [],
    tasks=self.active_track.tickets
   )
-  project_manager.save_track_state(self.active_track.id, state, self.ui_files_base_dir)
+  project_manager.save_track_state(self.active_track.id, state, self.active_project_root)
 

src/bg_shader.py

@@ -12,7 +12,7 @@ class BackgroundShader:
   self.ctx: Optional[nvg.Context] = None
 
  def render(self, width: float, height: float):
-  if not self.enabled:
+  if not self.enabled or width <= 0 or height <= 0:
    return
 
   # In imgui-bundle, hello_imgui handles the background.

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]:
   """
@@ -102,6 +109,15 @@ class AsyncEventQueue:
   """
   return self._queue.get()
 
+ def empty(self) -> bool:
+  """
+  Checks if the queue is empty.
+  
+  Returns:
+   True if the queue is empty, False otherwise.
+  """
+  return self._queue.empty()
+
  def task_done(self) -> None:
   """Signals that a formerly enqueued task is complete."""
   self._queue.task_done()

src/mcp_client.py

@@ -53,6 +53,8 @@ See Also:
 
 from __future__ import annotations
 import asyncio
+import json
+from src import models
 from pathlib import Path
 from typing import Optional, Callable, Any, cast
 import os
@@ -915,6 +917,126 @@ def get_ui_performance() -> str:
   return f"ERROR: Failed to retrieve UI performance: {str(e)}"
   # ------------------------------------------------------------------ tool dispatch
 
+class StdioMCPServer:
+ def __init__(self, config: models.MCPServerConfig):
+  self.config = config
+  self.name = config.name
+  self.proc = None
+  self.tools = {}
+  self._id_counter = 0
+  self._pending_requests = {}
+  self.status = 'idle'
+
+ def _get_id(self):
+  self._id_counter += 1
+  return self._id_counter
+
+ async def start(self):
+  self.status = 'starting'
+  self.proc = await asyncio.create_subprocess_exec(
+   self.config.command,
+   *self.config.args,
+   stdin=asyncio.subprocess.PIPE,
+   stdout=asyncio.subprocess.PIPE,
+   stderr=asyncio.subprocess.PIPE
+  )
+  asyncio.create_task(self._read_stderr())
+  await self.list_tools()
+  self.status = 'running'
+
+ async def stop(self):
+  if self.proc:
+   try:
+    if self.proc.stdin:
+     self.proc.stdin.close()
+     await self.proc.stdin.wait_closed()
+   except Exception:
+    pass
+   try:
+    self.proc.terminate()
+    await self.proc.wait()
+   except Exception:
+    pass
+   self.proc = None
+  self.status = 'idle'
+
+ async def _read_stderr(self):
+  while self.proc and not self.proc.stdout.at_eof():
+   line = await self.proc.stderr.readline()
+   if line:
+    print(f'[MCP:{self.name}:err] {line.decode().strip()}')
+
+ async def _send_request(self, method: str, params: dict = None):
+  req_id = self._get_id()
+  request = {
+   'jsonrpc': '2.0',
+   'id': req_id,
+   'method': method,
+   'params': params or {}
+  }
+  self.proc.stdin.write(json.dumps(request).encode() + b'\n')
+  await self.proc.stdin.drain()
+  
+  # Simplistic wait for response - in real use, we'd need a read loop
+  # For now, we'll read one line and hope it's ours (fragile, but for MVP)
+  line = await self.proc.stdout.readline()
+  if line:
+   resp = json.loads(line.decode())
+   return resp.get('result')
+  return None
+
+ async def list_tools(self):
+  result = await self._send_request('tools/list')
+  if result and 'tools' in result:
+   for t in result['tools']:
+    self.tools[t['name']] = t
+  return self.tools
+
+ async def call_tool(self, name: str, arguments: dict):
+  result = await self._send_request('tools/call', {'name': name, 'arguments': arguments})
+  if result and 'content' in result:
+   return '\n'.join([c.get('text', '') for c in result['content'] if c.get('type') == 'text'])
+  return str(result)
+
+class ExternalMCPManager:
+ def __init__(self):
+  self.servers = {}
+
+ async def add_server(self, config: models.MCPServerConfig):
+  if config.url:
+   # RemoteMCPServer placeholder
+   return
+  server = StdioMCPServer(config)
+  await server.start()
+  self.servers[config.name] = server
+
+ async def stop_all(self):
+  for server in self.servers.values():
+   await server.stop()
+  self.servers = {}
+
+ def get_all_tools(self) -> dict:
+  all_tools = {}
+  for sname, server in self.servers.items():
+   for tname, tool in server.tools.items():
+    all_tools[tname] = {**tool, 'server': sname, 'server_status': server.status}
+  return all_tools
+
+ def get_servers_status(self) -> dict[str, str]:
+  return {name: server.status for name, server in self.servers.items()}
+
+ async def async_dispatch(self, tool_name: str, tool_input: dict) -> str:
+  for server in self.servers.values():
+   if tool_name in server.tools:
+    return await server.call_tool(tool_name, tool_input)
+  return f'Error: External tool {tool_name} not found.'
+
+_external_mcp_manager = ExternalMCPManager()
+
+def get_external_mcp_manager() -> ExternalMCPManager:
+ global _external_mcp_manager
+ return _external_mcp_manager
+
 TOOL_NAMES: set[str] = {"read_file", "list_directory", "search_files", "get_file_summary", "py_get_skeleton", "py_get_code_outline", "py_get_definition", "get_git_diff", "web_search", "fetch_url", "get_ui_performance", "get_file_slice", "set_file_slice", "edit_file", "py_update_definition", "py_get_signature", "py_set_signature", "py_get_class_summary", "py_get_var_declaration", "py_set_var_declaration", "py_find_usages", "py_get_imports", "py_check_syntax", "py_get_hierarchy", "py_get_docstring", "get_tree"}
 
 def dispatch(tool_name: str, tool_input: dict[str, Any]) -> str:
@@ -987,17 +1109,29 @@ def dispatch(tool_name: str, tool_input: dict[str, Any]) -> str:
  return f"ERROR: unknown MCP tool '{tool_name}'"
 
 async def async_dispatch(tool_name: str, tool_input: dict[str, Any]) -> str:
- """
- Dispatch an MCP tool call by name asynchronously. Returns the result as a string.
- """
- # Run blocking I/O bound tools in a thread to allow parallel execution via asyncio.gather
- return await asyncio.to_thread(dispatch, tool_name, tool_input)
+ # Check native tools
+ native_names = {t['name'] for t in MCP_TOOL_SPECS}
+ if tool_name in native_names:
+  return await asyncio.to_thread(dispatch, tool_name, tool_input)
+ 
+ # Check external tools
+ if tool_name in get_external_mcp_manager().get_all_tools():
+  return await get_external_mcp_manager().async_dispatch(tool_name, tool_input)
+  
+ return f'ERROR: unknown MCP tool {tool_name}'
 
 
 
 def get_tool_schemas() -> list[dict[str, Any]]:
- """Returns the list of tool specifications for the AI."""
- return list(MCP_TOOL_SPECS)
+ res = list(MCP_TOOL_SPECS)
+ manager = get_external_mcp_manager()
+ for tname, tinfo in manager.get_all_tools().items():
+  res.append({
+   'name': tname,
+   'description': tinfo.get('description', ''),
+   'parameters': tinfo.get('inputSchema', {'type': 'object', 'properties': {}})
+  })
+ return res
 
 
 # ------------------------------------------------------------------ tool schema helpers

src/models.py

@@ -37,6 +37,8 @@ See Also:
  - src/project_manager.py for persistence layer
 """
 from __future__ import annotations
+import json
+import os
 import tomllib
 import datetime
 from dataclasses import dataclass, field
@@ -46,6 +48,13 @@ from src.paths import get_config_path
 
 CONFIG_PATH = get_config_path()
 
+def _clean_nones(data: Any) -> Any:
+ if isinstance(data, dict):
+  return {k: _clean_nones(v) for k, v in data.items() if v is not None}
+ elif isinstance(data, list):
+  return [_clean_nones(v) for v in data if v is not None]
+ return data
+
 def load_config() -> dict[str, Any]:
  with open(CONFIG_PATH, "rb") as f:
   return tomllib.load(f)
@@ -53,6 +62,7 @@ def load_config() -> dict[str, Any]:
 def save_config(config: dict[str, Any]) -> None:
  import tomli_w
  import sys
+ config = _clean_nones(config)
  sys.stderr.write(f"[DEBUG] Saving config. Theme: {config.get('theme')}\n")
  sys.stderr.flush()
  with open(CONFIG_PATH, "wb") as f:
@@ -101,6 +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 = ""
@@ -118,11 +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
@@ -229,8 +259,6 @@ class Track:
   )
 
 
-@dataclass
-@dataclass
 @dataclass
 class WorkerContext:
  ticket_id: str
@@ -329,12 +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
@@ -343,6 +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
@@ -438,6 +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]:
@@ -480,6 +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
@@ -513,5 +547,58 @@ 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
+ command: Optional[str] = None
+ args: List[str] = field(default_factory=list)
+ url: Optional[str] = None
+ auto_start: bool = False
+
+ def to_dict(self) -> Dict[str, Any]:
+  res = {'auto_start': self.auto_start}
+  if self.command: res['command'] = self.command
+  if self.args: res['args'] = self.args
+  if self.url: res['url'] = self.url
+  return res
+
+ @classmethod
+ def from_dict(cls, name: str, data: Dict[str, Any]) -> 'MCPServerConfig':
+  return cls(
+   name=name,
+   command=data.get('command'),
+   args=data.get('args', []),
+   url=data.get('url'),
+   auto_start=data.get('auto_start', False),
   )
 
+@dataclass
+class MCPConfiguration:
+ mcpServers: Dict[str, MCPServerConfig] = field(default_factory=dict)
+
+ def to_dict(self) -> Dict[str, Any]:
+  return {
+   'mcpServers': {name: cfg.to_dict() for name, cfg in self.mcpServers.items()}
+  }
+
+ @classmethod
+ def from_dict(cls, data: Dict[str, Any]) -> 'MCPConfiguration':
+  raw_servers = data.get('mcpServers', {})
+  parsed_servers = {
+   name: MCPServerConfig.from_dict(name, cfg)
+   for name, cfg in raw_servers.items()
+  }
+  return cls(mcpServers=parsed_servers)
+
+def load_mcp_config(path: str) -> MCPConfiguration:
+ if not os.path.exists(path):
+  return MCPConfiguration()
+ with open(path, 'r', encoding='utf-8') as f:
+  try:
+   data = json.load(f)
+   return MCPConfiguration.from_dict(data)
+  except Exception:
+   return MCPConfiguration()
+

src/paths.py

@@ -6,29 +6,28 @@ This module provides centralized path resolution for all configurable paths in t
 
 Environment Variables:
  SLOP_CONFIG: Path to config.toml
- SLOP_CONDUCTOR_DIR: Path to conductor directory
  SLOP_LOGS_DIR: Path to logs directory
  SLOP_SCRIPTS_DIR: Path to generated scripts directory
 
 Configuration (config.toml):
  [paths]
- conductor_dir = "conductor"
  logs_dir = "logs/sessions"
  scripts_dir = "scripts/generated"
 
 Path Functions:
  get_config_path() -> Path to config.toml
- get_conductor_dir() -> Path to conductor directory
+ get_conductor_dir(project_path=None) -> Path to conductor directory
  get_logs_dir() -> Path to logs/sessions
  get_scripts_dir() -> Path to scripts/generated
- get_tracks_dir() -> Path to conductor/tracks
- get_track_state_dir(track_id) -> Path to conductor/tracks/<track_id>
- get_archive_dir() -> Path to conductor/archive
+ get_tracks_dir(project_path=None) -> Path to conductor/tracks
+ get_track_state_dir(track_id, project_path=None) -> Path to conductor/tracks/<track_id>
+ get_archive_dir(project_path=None) -> Path to conductor/archive
 
 Resolution Order:
- 1. Check environment variable
- 2. Check config.toml [paths] section
- 3. Fall back to default
+ 1. Check project-specific manual_slop.toml (for conductor paths)
+ 2. Check environment variable (for logs/scripts)
+ 3. Check config.toml [paths] section (for logs/scripts)
+ 4. Fall back to default
 
 Usage:
  from src.paths import get_logs_dir, get_scripts_dir
@@ -44,16 +43,18 @@ See Also:
 from pathlib import Path
 import os
 import tomllib
-from typing import Optional
+from typing import Optional, Any
 
 _RESOLVED: dict[str, Path] = {}
 
 def get_config_path() -> Path:
  root_dir = Path(__file__).resolve().parent.parent
  return Path(os.environ.get("SLOP_CONFIG", root_dir / "config.toml"))
+
 def get_global_presets_path() -> Path:
  root_dir = Path(__file__).resolve().parent.parent
  return Path(os.environ.get("SLOP_GLOBAL_PRESETS", root_dir / "presets.toml"))
+
 def get_project_presets_path(project_root: Path) -> Path:
  return project_root / "project_presets.toml"
 
@@ -72,21 +73,50 @@ def get_project_personas_path(project_root: Path) -> Path:
  return project_root / "project_personas.toml"
 
 def _resolve_path(env_var: str, config_key: str, default: str) -> Path:
+ root_dir = Path(__file__).resolve().parent.parent
+ p = None
  if env_var in os.environ:
-  return Path(os.environ[env_var])
- try:
-  with open(get_config_path(), "rb") as f:
-   cfg = tomllib.load(f)
-  if "paths" in cfg and config_key in cfg["paths"]:
-   return Path(cfg["paths"][config_key])
- except FileNotFoundError:
-  pass
- return Path(default)
+  p = Path(os.environ[env_var])
+ else:
+  try:
+   with open(get_config_path(), "rb") as f:
+    cfg = tomllib.load(f)
+   if "paths" in cfg and config_key in cfg["paths"]:
+    p = Path(cfg["paths"][config_key])
+  except (FileNotFoundError, tomllib.TOMLDecodeError):
+   pass
+ if p is None:
+  p = Path(default)
+ if not p.is_absolute():
+  return root_dir / p
+ return p
 
-def get_conductor_dir() -> Path:
- if "conductor_dir" not in _RESOLVED:
-  _RESOLVED["conductor_dir"] = _resolve_path("SLOP_CONDUCTOR_DIR", "conductor_dir", "conductor")
- return _RESOLVED["conductor_dir"]
+def _get_project_conductor_dir_from_toml(project_root: Path) -> Optional[Path]:
+ # Look for manual_slop.toml in project_root
+ toml_path = project_root / 'manual_slop.toml'
+ if not toml_path.exists(): return None
+ try:
+  with open(toml_path, 'rb') as f:
+   data = tomllib.load(f)
+  # Check [conductor] dir = '...'
+  c_dir = data.get('conductor', {}).get('dir')
+  if c_dir:
+   p = Path(c_dir)
+   if not p.is_absolute(): p = project_root / p
+   return p.resolve()
+ except: pass
+ return None
+
+def get_conductor_dir(project_path: Optional[str] = None) -> Path:
+ if not project_path:
+  # Fallback for legacy/tests, but we should avoid this
+  return Path('conductor').resolve()
+ 
+ project_root = Path(project_path).resolve()
+ p = _get_project_conductor_dir_from_toml(project_root)
+ if p: return p
+ 
+ return (project_root / "conductor").resolve()
 
 def get_logs_dir() -> Path:
  if "logs_dir" not in _RESOLVED:
@@ -98,16 +128,37 @@ def get_scripts_dir() -> Path:
   _RESOLVED["scripts_dir"] = _resolve_path("SLOP_SCRIPTS_DIR", "scripts_dir", "scripts/generated")
  return _RESOLVED["scripts_dir"]
 
-def get_tracks_dir() -> Path:
- return get_conductor_dir() / "tracks"
+def get_tracks_dir(project_path: Optional[str] = None) -> Path:
+ return get_conductor_dir(project_path) / "tracks"
 
-def get_track_state_dir(track_id: str) -> Path:
- return get_tracks_dir() / track_id
+def get_track_state_dir(track_id: str, project_path: Optional[str] = None) -> Path:
+ return get_tracks_dir(project_path) / track_id
 
-def get_archive_dir() -> Path:
- return get_conductor_dir() / "archive"
+def get_archive_dir(project_path: Optional[str] = None) -> Path:
+ return get_conductor_dir(project_path) / "archive"
+
+def _resolve_path_info(env_var: str, config_key: str, default: str) -> dict[str, Any]:
+ if env_var in os.environ:
+  return {'path': Path(os.environ[env_var]).resolve(), 'source': f'env:{env_var}'}
+ try:
+  with open(get_config_path(), 'rb') as f:
+   cfg = tomllib.load(f)
+  if 'paths' in cfg and config_key in cfg['paths']:
+   p = Path(cfg['paths'][config_key])
+   if not p.is_absolute():
+    p = (Path(__file__).resolve().parent.parent / p).resolve()
+   return {'path': p, 'source': 'config.toml'}
+ except: pass
+ root_dir = Path(__file__).resolve().parent.parent
+ p = (root_dir / default).resolve()
+ return {'path': p, 'source': 'default'}
+
+def get_full_path_info() -> dict[str, dict[str, Any]]:
+ return {
+  'logs_dir': _resolve_path_info('SLOP_LOGS_DIR', 'logs_dir', 'logs/sessions'),
+  'scripts_dir': _resolve_path_info('SLOP_SCRIPTS_DIR', 'scripts_dir', 'scripts/generated')
+ }
 
 def reset_resolved() -> None:
  """For testing only - clear cached resolutions."""
  _RESOLVED.clear()
-

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":       {
@@ -196,6 +205,7 @@ def save_project(proj: dict[str, Any], path: Union[str, Path], disc_data: Option
    disc_data = proj["discussion"]
   proj = dict(proj)
   del proj["discussion"]
+ proj = clean_nones(proj)
  with open(path, "wb") as f:
   tomli_w.dump(proj, f)
  if disc_data:
@@ -230,22 +240,44 @@ 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:
  """
     Saves a TrackState object to conductor/tracks/<track_id>/state.toml.
     """
- track_dir = Path(base_dir) / paths.get_track_state_dir(track_id)
+ track_dir = paths.get_track_state_dir(track_id, project_path=str(base_dir))
  track_dir.mkdir(parents=True, exist_ok=True)
  state_file = track_dir / "state.toml"
  data = clean_nones(state.to_dict())
@@ -257,7 +289,7 @@ def load_track_state(track_id: str, base_dir: Union[str, Path] = ".") -> Optiona
     Loads a TrackState object from conductor/tracks/<track_id>/state.toml.
     """
  from src.models import TrackState
- state_file = Path(base_dir) / paths.get_track_state_dir(track_id) / "state.toml"
+ state_file = paths.get_track_state_dir(track_id, project_path=str(base_dir)) / 'state.toml'
  if not state_file.exists():
   return None
  with open(state_file, "rb") as f:
@@ -302,7 +334,7 @@ def get_all_tracks(base_dir: Union[str, Path] = ".") -> list[dict[str, Any]]:
     Handles missing or malformed metadata.json or state.toml by falling back
     to available info or defaults.
     """
- tracks_dir = Path(base_dir) / paths.get_tracks_dir()
+ tracks_dir = paths.get_tracks_dir(project_path=str(base_dir))
  if not tracks_dir.exists():
   return []
  results: list[dict[str, Any]] = []
@@ -392,3 +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/session_logger.py

@@ -112,6 +112,11 @@ def close_session() -> None:
  except Exception as e:
   print(f"Warning: Could not update auto-whitelist on close: {e}")
 
+def reset_session(label: Optional[str] = None) -> None:
+ """Closes the current session and opens a new one with the given label."""
+ close_session()
+ open_session(label)
+
 def log_api_hook(method: str, path: str, payload: str) -> None:
  """Log an API hook invocation."""
  if _api_fh is None:

src/shader_manager.py

@@ -0,0 +1,153 @@
+import OpenGL.GL as gl
+
+class ShaderManager:
+ def __init__(self):
+  self.program = None
+  self.bg_program = None
+  self.pp_program = None
+
+ def compile_shader(self, vertex_src: str, fragment_src: str) -> int:
+  program = gl.glCreateProgram()
+  
+  def _compile(src, shader_type):
+   shader = gl.glCreateShader(shader_type)
+   gl.glShaderSource(shader, src)
+   gl.glCompileShader(shader)
+   
+   if not gl.glGetShaderiv(shader, gl.GL_COMPILE_STATUS):
+    info_log = gl.glGetShaderInfoLog(shader)
+    if hasattr(info_log, "decode"):
+     info_log = info_log.decode()
+    raise RuntimeError(f"Shader compilation failed: {info_log}")
+   return shader
+
+  vert_shader = _compile(vertex_src, gl.GL_VERTEX_SHADER)
+  frag_shader = _compile(fragment_src, gl.GL_FRAGMENT_SHADER)
+  
+  gl.glAttachShader(program, vert_shader)
+  gl.glAttachShader(program, frag_shader)
+  gl.glLinkProgram(program)
+  
+  if not gl.glGetProgramiv(program, gl.GL_LINK_STATUS):
+   info_log = gl.glGetProgramInfoLog(program)
+   if hasattr(info_log, "decode"):
+    info_log = info_log.decode()
+   raise RuntimeError(f"Program linking failed: {info_log}")
+  
+  gl.glDeleteShader(vert_shader)
+  gl.glDeleteShader(frag_shader)
+  
+  self.program = program
+  return program
+
+ def update_uniforms(self, uniforms: dict):
+  if self.program is None:
+   return
+  
+  for name, value in uniforms.items():
+   loc = gl.glGetUniformLocation(self.program, name)
+   if loc == -1:
+    continue
+   
+   if isinstance(value, float):
+    gl.glUniform1f(loc, value)
+   elif isinstance(value, int):
+    gl.glUniform1i(loc, value)
+   elif isinstance(value, (list, tuple)):
+    if len(value) == 2:
+     gl.glUniform2f(loc, value[0], value[1])
+    elif len(value) == 3:
+     gl.glUniform3f(loc, value[0], value[1], value[2])
+    elif len(value) == 4:
+     gl.glUniform4f(loc, value[0], value[1], value[2], value[3])
+
+ def setup_background_shader(self):
+  vertex_src = """
+#version 330 core
+const vec2 positions[4] = vec2[](
+ vec2(-1.0, -1.0),
+ vec2( 1.0, -1.0),
+ vec2(-1.0,  1.0),
+ vec2( 1.0,  1.0)
+);
+void main() {
+ gl_Position = vec4(positions[gl_VertexID], 0.0, 1.0);
+}
+"""
+  fragment_src = """
+#version 330 core
+uniform float u_time;
+uniform vec2 u_resolution;
+out vec4 FragColor;
+void main() {
+ vec2 uv = gl_FragCoord.xy / u_resolution.xy;
+ vec3 col = 0.5 + 0.5 * cos(u_time + uv.xyx + vec3(0, 2, 4));
+ FragColor = vec4(col, 1.0);
+}
+"""
+  self.bg_program = self.compile_shader(vertex_src, fragment_src)
+
+ def render_background(self, width, height, time):
+  if not self.bg_program:
+   return
+  gl.glUseProgram(self.bg_program)
+  u_time_loc = gl.glGetUniformLocation(self.bg_program, "u_time")
+  if u_time_loc != -1:
+   gl.glUniform1f(u_time_loc, float(time))
+  u_res_loc = gl.glGetUniformLocation(self.bg_program, "u_resolution")
+  if u_res_loc != -1:
+   gl.glUniform2f(u_res_loc, float(width), float(height))
+  gl.glDrawArrays(gl.GL_TRIANGLE_STRIP, 0, 4)
+  gl.glUseProgram(0)
+
+ def setup_post_process_shader(self):
+  vertex_src = """
+#version 330 core
+const vec2 positions[4] = vec2[](
+ vec2(-1.0, -1.0),
+ vec2( 1.0, -1.0),
+ vec2(-1.0,  1.0),
+ vec2( 1.0,  1.0)
+);
+const vec2 uvs[4] = vec2[](
+ vec2(0.0, 0.0),
+ vec2(1.0, 0.0),
+ vec2(0.0, 1.0),
+ vec2(1.0, 1.0)
+);
+out vec2 v_uv;
+void main() {
+ gl_Position = vec4(positions[gl_VertexID], 0.0, 1.0);
+ v_uv = uvs[gl_VertexID];
+}
+"""
+  fragment_src = """
+#version 330 core
+in vec2 v_uv;
+uniform sampler2D u_texture;
+uniform float u_time;
+out vec4 FragColor;
+void main() {
+ vec4 color = texture(u_texture, v_uv);
+ float scanline = sin(v_uv.y * 800.0 + u_time * 2.0) * 0.04;
+ color.rgb -= scanline;
+ FragColor = color;
+}
+"""
+  self.pp_program = self.compile_shader(vertex_src, fragment_src)
+
+ def render_post_process(self, texture_id, width, height, time):
+  if not self.pp_program:
+   return
+  gl.glUseProgram(self.pp_program)
+  gl.glActiveTexture(gl.GL_TEXTURE0)
+  gl.glBindTexture(gl.GL_TEXTURE_2D, texture_id)
+  u_tex_loc = gl.glGetUniformLocation(self.pp_program, "u_texture")
+  if u_tex_loc != -1:
+   gl.glUniform1i(u_tex_loc, 0)
+  u_time_loc = gl.glGetUniformLocation(self.pp_program, "u_time")
+  if u_time_loc != -1:
+   gl.glUniform1f(u_time_loc, float(time))
+  gl.glDrawArrays(gl.GL_TRIANGLE_STRIP, 0, 4)
+  gl.glBindTexture(gl.GL_TEXTURE_2D, 0)
+  gl.glUseProgram(0)

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/theme.py

@@ -268,6 +268,12 @@ _current_palette:  str          = "DPG Default"
 _current_font_path: str         = ""
 _current_font_size: float       = 14.0
 _current_scale:    float        = 1.0
+_shader_config: dict[str, Any]  = {
+ "crt": False,
+ "bloom": False,
+ "bg": "none",
+ "custom_window_frame": False,
+}
 
 # ------------------------------------------------------------------ public API
 
@@ -286,6 +292,14 @@ def get_current_font_size() -> float:
 def get_current_scale() -> float:
  return _current_scale
 
+def get_shader_config(key: str) -> Any:
+ """Get a specific shader configuration value."""
+ return _shader_config.get(key)
+
+def get_window_frame_config() -> bool:
+ """Get the window frame configuration."""
+ return _shader_config.get("custom_window_frame", False)
+
 def get_palette_colours(name: str) -> dict[str, Any]:
  """Return a copy of the colour dict for the named palette."""
  return dict(_PALETTES.get(name, {}))
@@ -388,4 +402,9 @@ def load_from_config(config: dict[str, Any]) -> None:
  if font_path:
   apply_font(font_path, font_size)
  set_scale(scale)
+ global _shader_config
+ _shader_config["crt"] = t.get("shader_crt", False)
+ _shader_config["bloom"] = t.get("shader_bloom", False)
+ _shader_config["bg"] = t.get("shader_bg", "none")
+ _shader_config["custom_window_frame"] = t.get("custom_window_frame", False)
 

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()

test_presets.toml

@@ -0,0 +1,2 @@
+[presets.ModalPreset]
+system_prompt = "Modal Content"

tests/conftest.py

@@ -200,14 +200,29 @@ def live_gui() -> Generator[tuple[subprocess.Popen, str], None, None]:
  temp_workspace.mkdir(parents=True, exist_ok=True)
  
  # Create minimal project files to avoid cluttering root
- (temp_workspace / "manual_slop.toml").write_text("[project]\nname = 'TestProject'\n", encoding="utf-8")
+ (temp_workspace / "manual_slop.toml").write_text("[project]\nname = 'TestProject'\n\n[conductor]\ndir = 'conductor'\n", encoding="utf-8")
  (temp_workspace / "conductor" / "tracks").mkdir(parents=True, exist_ok=True)
  
+ # Create a local config.toml in temp_workspace
+ config_content = {
+  'ai': {'provider': 'gemini', 'model': 'gemini-2.5-flash-lite'},
+  'projects': {
+   'paths': [str((temp_workspace / 'manual_slop.toml').absolute())],
+   'active': str((temp_workspace / 'manual_slop.toml').absolute())
+  },
+  'paths': {
+   'logs_dir': str((temp_workspace / "logs").absolute()),
+   'scripts_dir': str((temp_workspace / "scripts" / "generated").absolute())
+  }
+ }
+ import tomli_w
+ with open(temp_workspace / 'config.toml', 'wb') as f:
+  tomli_w.dump(config_content, f)
+ 
  # Resolve absolute paths for shared resources
  project_root = Path(os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
  config_file = temp_workspace / "config.toml"
- if not config_file.exists():
-  config_file = project_root / "config.toml"
+ 
  cred_file = project_root / "credentials.toml"
  mcp_file = project_root / "mcp_env.toml"
  

tests/test_api_hook_extensions.py

@@ -36,6 +36,7 @@ def test_app_processes_new_actions() -> None:
  with patch('src.models.load_config', return_value={}), \
    patch('src.performance_monitor.PerformanceMonitor'), \
    patch('src.session_logger.open_session'), \
+   patch('src.session_logger.reset_session'), \
    patch('src.app_controller.AppController._prune_old_logs'), \
    patch('src.app_controller.AppController._load_active_project'):
   app = gui_2.App()

tests/test_app_controller_mcp.py

@@ -0,0 +1,106 @@
+import os
+import json
+import pytest
+from pathlib import Path
+from src.app_controller import AppController
+from src import models
+
+@pytest.fixture
+def controller(tmp_path):
+    # Setup mock config and project files
+    config_path = tmp_path / "config.toml"
+    project_path = tmp_path / "project.toml"
+    mcp_config_path = tmp_path / "mcp_config.json"
+    
+    config_data = {
+        "ai": {
+            "mcp_config_path": str(mcp_config_path)
+        },
+        "projects": {
+            "paths": [str(project_path)],
+            "active": str(project_path)
+        }
+    }
+    
+    project_data = {
+        "project": {
+            "name": "test-project",
+            "mcp_config_path": "project_mcp.json" # Relative path
+        }
+    }
+    
+    mcp_data = {
+        "mcpServers": {
+            "global-server": {"command": "echo"}
+        }
+    }
+    
+    project_mcp_data = {
+        "mcpServers": {
+            "project-server": {"command": "echo"}
+        }
+    }
+    
+    # We can't easily use models.save_config because it uses a hardcoded path
+    # But AppController.init_state calls models.load_config() which uses CONFIG_PATH
+    
+    return AppController()
+
+def test_app_controller_mcp_loading(tmp_path, monkeypatch):
+    # Mock CONFIG_PATH to point to our temp config
+    config_file = tmp_path / "config.toml"
+    monkeypatch.setattr(models, "CONFIG_PATH", str(config_file))
+    
+    mcp_global_file = tmp_path / "mcp_global.json"
+    mcp_global_file.write_text(json.dumps({"mcpServers": {"global": {"command": "echo"}}}))
+    
+    config_content = f"""
+[ai]
+mcp_config_path = "{mcp_global_file.as_posix()}"
+[projects]
+paths = []
+active = ""
+"""
+    config_file.write_text(config_content)
+    
+    ctrl = AppController()
+    # Mock _load_active_project to not do anything for now
+    monkeypatch.setattr(ctrl, "_load_active_project", lambda: None)
+    ctrl.project = {}
+    
+    ctrl.init_state()
+    
+    assert "global" in ctrl.mcp_config.mcpServers
+    assert ctrl.mcp_config.mcpServers["global"].command == "echo"
+
+def test_app_controller_mcp_project_override(tmp_path, monkeypatch):
+    config_file = tmp_path / "config.toml"
+    monkeypatch.setattr(models, "CONFIG_PATH", str(config_file))
+    
+    project_file = tmp_path / "project.toml"
+    mcp_project_file = tmp_path / "mcp_project.json"
+    mcp_project_file.write_text(json.dumps({"mcpServers": {"project": {"command": "echo"}}}))
+    
+    config_content = f"""
+[ai]
+mcp_config_path = "non-existent.json"
+[projects]
+paths = ["{project_file.as_posix()}"]
+active = "{project_file.as_posix()}"
+"""
+    config_file.write_text(config_content)
+    
+    ctrl = AppController()
+    ctrl.active_project_path = str(project_file)
+    ctrl.project = {
+        "project": {
+            "mcp_config_path": "mcp_project.json"
+        }
+    }
+    # Mock _load_active_project to keep our manual project dict
+    monkeypatch.setattr(ctrl, "_load_active_project", lambda: None)
+    
+    ctrl.init_state()
+    
+    assert "project" in ctrl.mcp_config.mcpServers
+    assert "non-existent" not in ctrl.mcp_config.mcpServers

tests/test_arch_boundary_phase2.py

@@ -47,6 +47,7 @@ class TestArchBoundaryPhase2(unittest.TestCase):
     with patch('src.models.load_config', return_value={}), \
        patch('src.performance_monitor.PerformanceMonitor'), \
        patch('src.session_logger.open_session'), \
+       patch('src.session_logger.reset_session'), \
        patch('src.app_controller.AppController._prune_old_logs'), \
        patch('src.app_controller.AppController._init_ai_and_hooks'):
       controller = AppController()
@@ -69,6 +70,7 @@ class TestArchBoundaryPhase2(unittest.TestCase):
     with patch('src.models.load_config', return_value={}), \
        patch('src.performance_monitor.PerformanceMonitor'), \
        patch('src.session_logger.open_session'), \
+       patch('src.session_logger.reset_session'), \
        patch('src.app_controller.AppController._prune_old_logs'), \
        patch('src.app_controller.AppController._init_ai_and_hooks'):
       controller = AppController()

tests/test_context_composition_panel.py

@@ -0,0 +1,42 @@
+import pytest
+import inspect
+
+
+def test_context_composition_panel_replaces_placeholder():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._gui_func)
+    assert "_render_context_composition_placeholder" not in source, (
+        "Placeholder should be replaced"
+    )
+    assert "_render_context_composition_panel" in source, (
+        "Should have _render_context_composition_panel"
+    )
+
+
+def test_context_composition_has_save_load_buttons():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._render_context_composition_panel)
+    assert "Save as Preset" in source or "save" in source.lower(), (
+        "Should have Save functionality"
+    )
+    assert "Load Preset" in source or "load" in source.lower(), (
+        "Should have Load functionality"
+    )
+
+
+def test_context_composition_shows_files():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._render_context_composition_panel)
+    assert "files" in source.lower() or "Files" in source, "Should show files"
+
+
+def test_context_composition_has_preset_list():
+    import src.gui_2 as gui_2
+
+    source = inspect.getsource(gui_2.App._render_context_composition_panel)
+    assert "context_presets" in source or "preset" in source.lower(), (
+        "Should reference presets"
+    )

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_dynamic_background.py

@@ -0,0 +1,33 @@
+import pytest
+from unittest.mock import patch, MagicMock
+
+def test_dynamic_background_rendering():
+ # Mock OpenGL before importing
+ with patch("src.shader_manager.gl") as mock_gl:
+  from src.shader_manager import ShaderManager
+  
+  # Setup mock return values
+  mock_gl.glCreateProgram.return_value = 1
+  mock_gl.glCreateShader.return_value = 2
+  mock_gl.glGetShaderiv.return_value = 1 # GL_TRUE
+  mock_gl.glGetProgramiv.return_value = 1 # GL_TRUE
+  mock_gl.glGetUniformLocation.return_value = 10
+  
+  manager = ShaderManager()
+  manager.setup_background_shader()
+  
+  # Verify background program was created
+  assert manager.bg_program == 1
+  assert mock_gl.glCreateProgram.called
+  
+  # Render background
+  manager.render_background(800, 600, 1.0)
+  
+  # Verify OpenGL calls
+  mock_gl.glUseProgram.assert_any_call(1)
+  mock_gl.glDrawArrays.assert_called_with(mock_gl.GL_TRIANGLE_STRIP, 0, 4)
+  mock_gl.glUseProgram.assert_any_call(0)
+  
+  # Verify uniforms were updated
+  mock_gl.glUniform1f.assert_called()
+  mock_gl.glUniform2f.assert_called()

tests/test_external_mcp.py

@@ -0,0 +1,55 @@
+import asyncio
+import json
+import sys
+import pytest
+from src import mcp_client
+from src import models
+
+@pytest.mark.asyncio
+async def test_external_mcp_real_process():
+    manager = mcp_client.ExternalMCPManager()
+    
+    # Use our mock script
+    mock_script = "scripts/mock_mcp_server.py"
+    config = models.MCPServerConfig(
+        name="real-mock", 
+        command="python", 
+        args=[mock_script]
+    )
+    
+    await manager.add_server(config)
+    
+    try:
+        tools = manager.get_all_tools()
+        assert "echo" in tools
+        assert tools["echo"]["server"] == "real-mock"
+        
+        result = await manager.async_dispatch("echo", {"hello": "world"})
+        assert "ECHO: {'hello': 'world'}" in result
+    finally:
+        await manager.stop_all()
+
+@pytest.mark.asyncio
+async def test_get_tool_schemas_includes_external():
+    manager = mcp_client.get_external_mcp_manager()
+    # Reset manager
+    await manager.stop_all()
+    
+    mock_script = "scripts/mock_mcp_server.py"
+    config = models.MCPServerConfig(
+        name="test-server", 
+        command="python", 
+        args=[mock_script]
+    )
+    
+    await manager.add_server(config)
+    
+    try:
+        schemas = mcp_client.get_tool_schemas()
+        echo_schema = next((s for s in schemas if s["name"] == "echo"), None)
+        
+        assert echo_schema is not None
+        assert echo_schema["description"] == "Echo input"
+        assert echo_schema["parameters"] == {"type": "object"}
+    finally:
+        await manager.stop_all()

tests/test_external_mcp_e2e.py

@@ -0,0 +1,67 @@
+import asyncio
+import json
+import os
+from pathlib import Path
+import pytest
+from src.app_controller import AppController
+from src import mcp_client
+from src import ai_client
+from src import models
+
+@pytest.mark.asyncio
+async def test_external_mcp_e2e_refresh_and_call(tmp_path, monkeypatch):
+ # 1. Setup mock config and mock server script
+ config_file = tmp_path / "config.toml"
+ monkeypatch.setattr(models, "CONFIG_PATH", str(config_file))
+ 
+ mock_script = Path("scripts/mock_mcp_server.py").absolute()
+ 
+ mcp_config_file = tmp_path / "mcp_config.json"
+ mcp_data = {
+  "mcpServers": {
+   "e2e-server": {
+    "command": "python",
+    "args": [str(mock_script)],
+    "auto_start": True
+   }
+  }
+ }
+ mcp_config_file.write_text(json.dumps(mcp_data))
+ 
+ config_content = f"""
+[ai]
+mcp_config_path = "{mcp_config_file.as_posix()}"
+[projects]
+paths = []
+active = ""
+"""
+ config_file.write_text(config_content)
+ 
+ # 2. Initialize AppController
+ ctrl = AppController()
+ monkeypatch.setattr(ctrl, "_load_active_project", lambda: None)
+ ctrl.project = {}
+ 
+ # We need to mock start_services or just manually call what we need
+ ctrl.init_state()
+ 
+ # Trigger refresh event manually (since we don't have the background thread running in unit test)
+ await ctrl.refresh_external_mcps()
+ 
+ # 3. Verify tools are discovered
+ manager = mcp_client.get_external_mcp_manager()
+ tools = manager.get_all_tools()
+ assert "echo" in tools
+ 
+ # 4. Mock pre_tool_callback to auto-approve
+ mock_pre_tool = lambda desc, base, qa: "Approved"
+ 
+ # 5. Call execute_single_tool_call_async (via ai_client)
+ name, cid, out, orig = await ai_client._execute_single_tool_call_async(
+  "echo", {"message": "hello"}, "id1", ".", mock_pre_tool, None, 0
+ )
+ 
+ assert "ECHO: {'message': 'hello'}" in out
+ 
+ # Cleanup
+ await manager.stop_all()

tests/test_external_mcp_hitl.py

@@ -0,0 +1,62 @@
+import asyncio
+import json
+import pytest
+from unittest.mock import MagicMock, patch, AsyncMock
+from src import ai_client
+from src import mcp_client
+from src import models
+
+@pytest.mark.asyncio
+async def test_external_mcp_hitl_approval():
+    # 1. Setup mock manager and server
+    mock_manager = mcp_client.ExternalMCPManager()
+    mock_server = AsyncMock()
+    mock_server.name = "test-server"
+    mock_server.tools = {"ext_tool": {"name": "ext_tool", "description": "desc"}}
+    mock_server.call_tool.return_value = "Success"
+    mock_manager.servers["test-server"] = mock_server
+    
+    with patch("src.mcp_client.get_external_mcp_manager", return_value=mock_manager):
+        # 2. Setup ai_client callbacks
+        mock_pre_tool = MagicMock(return_value="Approved")
+        ai_client.confirm_and_run_callback = mock_pre_tool
+        
+        # 3. Call _execute_single_tool_call_async
+        name = "ext_tool"
+        args = {"arg1": "val1"}
+        call_id = "call_123"
+        base_dir = "."
+        
+        # We need to pass the callback to the function
+        name, cid, out, orig_name = await ai_client._execute_single_tool_call_async(
+            name, args, call_id, base_dir, mock_pre_tool, None, 0
+        )
+        
+        # 4. Assertions
+        assert out == "Success"
+        mock_pre_tool.assert_called_once()
+        # Check description contains EXTERNAL MCP
+        call_args = mock_pre_tool.call_args[0]
+        assert "EXTERNAL MCP TOOL: ext_tool" in call_args[0]
+        assert "arg1: 'val1'" in call_args[0]
+
+@pytest.mark.asyncio
+async def test_external_mcp_hitl_rejection():
+    mock_manager = mcp_client.ExternalMCPManager()
+    mock_server = AsyncMock()
+    mock_server.name = "test-server"
+    mock_server.tools = {"ext_tool": {"name": "ext_tool"}}
+    mock_manager.servers["test-server"] = mock_server
+    
+    with patch("src.mcp_client.get_external_mcp_manager", return_value=mock_manager):
+        mock_pre_tool = MagicMock(return_value=None) # Rejection
+        
+        name = "ext_tool"
+        args = {"arg1": "val1"}
+        
+        name, cid, out, orig_name = await ai_client._execute_single_tool_call_async(
+            name, args, "id", ".", mock_pre_tool, None, 0
+        )
+        
+        assert out == "USER REJECTED: tool execution cancelled"
+        mock_server.call_tool.assert_not_called()

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_custom_window.py

@@ -0,0 +1,15 @@
+import pytest
+from unittest.mock import patch
+from src.gui_2 import App
+
+@patch("src.gui_2.immapp.run")
+@patch("src.gui_2.session_logger.close_session")
+@patch("src.gui_2.imgui.save_ini_settings_to_disk")
+@patch("sys.argv", ["gui_2.py"])
+def test_app_window_is_borderless(mock_save_ini, mock_close, mock_run):
+ app = App()
+ app.run()
+ 
+ assert app.runner_params is not None
+ # This assertion will fail initially because we haven't implemented it yet
+ assert getattr(app.runner_params.app_window_params, 'borderless', False) is True, "Window should be borderless"

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_events_v2.py

@@ -15,6 +15,7 @@ def mock_gui() -> App:
   patch('src.project_manager.migrate_from_legacy_config', return_value={}),
   patch('src.project_manager.save_project'),
   patch('src.session_logger.open_session'),
+  patch('src.session_logger.reset_session'),
   patch('src.app_controller.AppController._init_ai_and_hooks'),
   patch('src.app_controller.AppController._fetch_models')
  ):