checkpoint: track complete

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/product.md

@@ -17,7 +17,7 @@ For deep implementation details when planning or implementing tracks, consult `d
 ## Primary Use Cases
 
 - **Full Control over Vendor APIs:** Exposing detailed API metrics and configuring deep agent capabilities directly within the GUI.
-- **Context & Memory Management:** Better visualization and management of token usage and context memory. Includes granular per-file flags (**Auto-Aggregate**, **Force Full**) and a dedicated **'Context' role** for manual injections, allowing developers to optimize prompt limits with expert precision.
+- **Context & Memory Management:** Better visualization and management of token usage and context memory. Includes granular per-file flags (**Auto-Aggregate**, **Force Full**), a dedicated **'Context' role** for manual injections, and **Context Presets** for saving and loading named file/screenshot selections. Allows assigning specific context presets to MMA agent personas for granular cognitive load isolation.
 - **Manual "Vibe Coding" Assistant:** Serving as an auxiliary, multi-provider assistant that natively interacts with the codebase via sandboxed PowerShell scripts and MCP-like file tools, emphasizing manual developer oversight and explicit confirmation.
 
 ## Key Features
@@ -33,6 +33,7 @@ For deep implementation details when planning or implementing tracks, consult `d
     - **Track Browser:** Real-time visualization of all implementation tracks with status indicators and progress bars. Includes a dedicated **Active Track Summary** featuring a color-coded progress bar, precise ticket status breakdown (Completed, In Progress, Blocked, Todo), and dynamic **ETA estimation** based on historical completion times.
     - **Visual Task DAG:** An interactive, node-based visualizer for the active track's task dependencies using `imgui-node-editor`. Features color-coded state tracking (Ready, Running, Blocked, Done), drag-and-drop dependency creation, and right-click deletion.
     - **Strategy Visualization:** Dedicated real-time output streams for Tier 1 (Strategic Planning) and Tier 2/3 (Execution) agents, allowing the user to follow the agent's reasoning chains alongside the task DAG.
+    - **Agent-Focused Filtering:** Allows the user to focus the entire GUI (Session Hub, Discussion Hub, Comms) on a specific agent's activities and scoped context.
   - **Track-Scoped State Management:** Segregates discussion history and task progress into per-track state files. Supports **Project-Specific Conductor Directories**, defaulting to `./conductor` relative to each project's TOML file. Projects can define their own conductor path override in `manual_slop.toml` (`[conductor].dir`) via the Projects tab for isolated track management. This prevents global context pollution and ensures the Tech Lead session is isolated to the specific track's objective.
   **Native DAG Execution Engine:** Employs a Python-based Directed Acyclic Graph (DAG) engine to manage complex task dependencies. Supports automated topological sorting, robust cycle detection, and **transitive blocking propagation** (cascading `blocked` status to downstream dependents to prevent execution stalls).
 
@@ -54,6 +55,8 @@ For deep implementation details when planning or implementing tracks, consult `d
 - **High-Fidelity Selectable UI:** Most read-only labels and logs across the interface (including discussion history, comms payloads, tool outputs, and telemetry metrics) are now implemented as selectable text fields. This enables standard OS-level text selection and copying (Ctrl+C) while maintaining a high-density, non-editable aesthetic.
 - **High-Fidelity UI Rendering:** Employs advanced 3x font oversampling and sub-pixel positioning to ensure crisp, high-clarity text rendering across all resolutions, enhancing readability for dense logs and complex code fragments.
 - **Enhanced MMA Observability:** Worker streams and ticket previews now support direct text selection, allowing for easy extraction of specific logs or reasoning fragments during parallel execution.
+- **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 branching, timestamping, and specific git commit linkage per conversation.
 - **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.
@@ -66,7 +69,7 @@ For deep implementation details when planning or implementing tracks, consult `d
 - **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/`.
 - **Performance Diagnostics:** Comprehensive, conditional per-component profiling across the entire application. Features a dedicated **Diagnostics Panel** providing real-time telemetry for FPS, Frame Time, CPU usage, and **Detailed Component Timings** for all GUI panels and background threads, including automated threshold-based latency alerts.
 - **Automated UX Verification:** A robust IPC mechanism via API hooks and a modular simulation suite allows for human-like simulation walkthroughs and automated regression testing of the full GUI lifecycle across multiple specialized scenarios.
-- **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, and a high-fidelity **frosted glass (acrylic) background effect** for panels 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).
+- **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 & 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.

conductor/tech-stack.md

@@ -70,6 +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.
-- **Hybrid Shader Pipeline:** Utilizes an optimized `ImDrawList`-based batching technique to simulate UI effects such as soft shadows 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), dynamic backgrounds, and high-fidelity **frosted glass (acrylic) blurring** of the GUI panels via multi-pass Gaussian/Kawase filtering.
+- **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

@@ -35,8 +35,8 @@ This file tracks all major tracks for the project. Each track has its own detail
 7. [ ] **Track: Optimization pass for Data-Oriented Python heuristics**
     *Link: [./tracks/data_oriented_optimization_20260312/](./tracks/data_oriented_optimization_20260312/)*
 
-8. [ ] **Track: Rich Thinking Trace Handling**
+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/)*
+   *Link: [./tracks/thinking_trace_handling_20260313/](./tracks/thinking_trace_handling_20260313/)*
 
 ---
 
@@ -60,14 +60,14 @@ 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. [x] **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**
    *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.*
 
@@ -79,12 +79,9 @@ This file tracks all major tracks for the project. Each track has its own detail
     *Link: [./tracks/undo_redo_history_20260311/](./tracks/undo_redo_history_20260311/)*
     *Goal: Robust, non-provider based undo/redo for text inputs, UI controls, discussion mutations, and context management. Includes hotkey support and a history list view.*
 
-11. [ ] **Track: Advanced Text Viewer with Syntax Highlighting**
+11. [x] **Track: Advanced Text Viewer with Syntax Highlighting**
     *Link: [./tracks/text_viewer_rich_rendering_20260313/](./tracks/text_viewer_rich_rendering_20260313/)*
 
-12. [x] **Track: Frosted Glass Background Effect**
-    *Link: [./tracks/frosted_glass_20260313/](./tracks/frosted_glass_20260313/)*
-
 ---
 
 ### Additional Language Support
@@ -164,6 +161,10 @@ This file tracks all major tracks for the project. Each track has its own detail
 
 ### Completed / Archived
 
+-. [ ] ~~**Track: Frosted Glass Background Effect**~~ ***NOT WORTH THE PAIN***
+    *Link: [./tracks/frosted_glass_20260313/](./tracks/frosted_glass_20260313/)*
+
+
 - [x] **Track: External MCP Server Support** (Archived 2026-03-12)
 - [x] **Track: Project-Specific Conductor Directory** (Archived 2026-03-12)
 - [x] **Track: GUI Path Configuration in Context Hub** (Archived 2026-03-12)

conductor/tracks/frosted_glass_20260313/plan.md

@@ -1,26 +0,0 @@
-# Implementation Plan: Frosted Glass Background Effect
-
-## Phase 1: Shader Development & Integration [checkpoint: 55f3bd8]
-- [x] Task: Audit `src/shader_manager.py` to identify existing background/post-process integration points. [1328bc1]
-- [x] Task: Write Tests: Verify `ShaderManager` can compile and bind a multi-pass blur shader. [1328bc1]
-- [x] Task: Implement: Add `FrostedGlassShader` (GLSL) to `src/shader_manager.py`. [1328bc1]
-- [x] Task: Implement: Integrate the blur shader into the `ShaderManager` lifecycle. [1328bc1]
-- [x] Task: Conductor - User Manual Verification 'Phase 1: Shader Development & Integration' (Protocol in workflow.md) [55f3bd8]
-
-## Phase 2: Framebuffer Capture Pipeline [checkpoint: e9b7875]
-- [x] Task: Write Tests: Verify the FBO capture mechanism correctly samples the back buffer and stores it in a texture. [f297e7a]
-- [x] Task: Implement: Update `src/shader_manager.py` or `src/gui_2.py` to handle "pre-rendering" of the background into a texture for blurring. [f297e7a]
-- [x] Task: Implement: Ensure the blurred texture is updated every frame or on window move events. [f297e7a]
-- [x] Task: Conductor - User Manual Verification 'Phase 2: Framebuffer Capture Pipeline' (Protocol in workflow.md) [e9b7875]
-
-## Phase 3: GUI Integration & Rendering [checkpoint: cecbe22]
-- [x] Task: Write Tests: Verify that a mocked ImGui window successfully calls the frosted glass rendering logic. [cecbe22]
-- [x] Task: Implement: Create a `_render_frosted_background(self, pos, size)` helper in `src/gui_2.py`. [cecbe22]
-- [x] Task: Implement: Update panel rendering loops (e.g. `_gui_func`) to inject the frosted background before calling `imgui.begin()` for major panels. [cecbe22]
-- [x] Task: Conductor - User Manual Verification 'Phase 3: GUI Integration & Rendering' (Protocol in workflow.md) [cecbe22]
-
-## Phase 4: UI Controls & Configuration [checkpoint: cecbe22]
-- [x] Task: Write Tests: Verify that modifying blur uniforms via the Live Editor updates the shader state. [cecbe22]
-- [x] Task: Implement: Add "Frosted Glass" sliders (Blur, Tint, Opacity) to the **Shader Editor** in `src/gui_2.py`. [cecbe22]
-- [x] Task: Implement: Update `src/theme.py` to parse and store frosted glass settings from `config.toml`. [cecbe22]
-- [x] Task: Conductor - User Manual Verification 'Phase 4: UI Controls & Configuration' (Protocol in workflow.md) [cecbe22]

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

conductor/tracks/text_viewer_rich_rendering_20260313/plan.md

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

conductor/tracks/thinking_trace_handling_20260313/plan.md

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

config.toml

@@ -26,20 +26,20 @@ separate_tool_calls_panel = false
 bg_shader_enabled = false
 crt_filter_enabled = false
 separate_task_dag = false
-separate_usage_analytics = true
+separate_usage_analytics = false
 separate_tier1 = false
 separate_tier2 = false
 separate_tier3 = false
 separate_tier4 = false
-separate_external_tools = true
+separate_external_tools = false
 
 [gui.show_windows]
 "Context Hub" = true
 "Files & Media" = true
 "AI Settings" = true
-"MMA Dashboard" = true
+"MMA Dashboard" = false
 "Task DAG" = false
-"Usage Analytics" = true
+"Usage Analytics" = false
 "Tier 1" = false
 "Tier 2" = false
 "Tier 3" = false
@@ -52,24 +52,20 @@ separate_external_tools = true
 "Operations Hub" = true
 Message = false
 Response = true
-"Tool Calls" = true
+"Tool Calls" = false
 Theme = true
-"Log Management" = true
+"Log Management" = false
 Diagnostics = false
 "External Tools" = false
-"Shader Editor" = true
+"Shader Editor" = false
 
 [theme]
 palette = "Nord Dark"
 font_path = "C:/projects/manual_slop/assets/fonts/MapleMono-Regular.ttf"
-font_size = 16.0
+font_size = 18.0
 scale = 1.0
-transparency = 0.699999988079071
+transparency = 1.0
-child_transparency = 0.6899999976158142
+child_transparency = 1.0
-frosted_blur_radius = 29.68400001525879
-frosted_tint_intensity = 0.5659999847412109
-frosted_opacity = 0.5389999747276306
-frosted_glass_enabled = true
 
 [mma]
 max_workers = 4

manualslop_layout.ini

@@ -12,7 +12,7 @@ ViewportPos=43,95
 ViewportId=0x78C57832
 Size=897,649
 Collapsed=0
-DockId=0x00000005,0
+DockId=0x00000001,0
 
 [Window][Files]
 ViewportPos=3125,170
@@ -33,7 +33,7 @@ DockId=0x0000000A,0
 Pos=0,17
 Size=1680,730
 Collapsed=0
-DockId=0x00000005,0
+DockId=0x00000001,0
 
 [Window][Provider]
 ViewportPos=43,95
@@ -41,22 +41,23 @@ ViewportId=0x78C57832
 Pos=0,651
 Size=897,468
 Collapsed=0
-DockId=0x00000005,0
+DockId=0x00000001,0
 
 [Window][Message]
-Pos=661,1321
+Pos=711,694
 Size=716,455
 Collapsed=0
 
 [Window][Response]
-Pos=2437,925
+Pos=1946,1000
-Size=1111,773
+Size=1339,785
 Collapsed=0
 
 [Window][Tool Calls]
-Pos=1039,464
+Pos=1028,1668
-Size=587,510
+Size=1397,340
 Collapsed=0
+DockId=0x00000006,0
 
 [Window][Comms History]
 ViewportPos=43,95
@@ -73,10 +74,10 @@ Collapsed=0
 DockId=0xAFC85805,2
 
 [Window][Theme]
-Pos=2671,24
+Pos=0,1010
-Size=1169,2136
+Size=828,999
 Collapsed=0
-DockId=0x00000002,1
+DockId=0x00000002,2
 
 [Window][Text Viewer - Entry #7]
 Pos=379,324
@@ -84,16 +85,16 @@ Size=900,700
 Collapsed=0
 
 [Window][Diagnostics]
-Pos=1649,24
+Pos=2177,26
-Size=580,1284
+Size=1162,1777
 Collapsed=0
-DockId=0x00000004,2
+DockId=0x00000010,0
 
 [Window][Context Hub]
-Pos=0,1719
+Pos=0,1010
-Size=999,441
+Size=828,999
 Collapsed=0
-DockId=0x00000006,0
+DockId=0x00000002,1
 
 [Window][AI Settings Hub]
 Pos=406,17
@@ -102,45 +103,45 @@ Collapsed=0
 DockId=0x0000000D,0
 
 [Window][Discussion Hub]
-Pos=1762,24
+Pos=1768,26
-Size=907,2136
+Size=1263,1983
 Collapsed=0
-DockId=0x00000011,0
+DockId=0x00000013,0
 
 [Window][Operations Hub]
-Pos=1001,24
+Pos=830,26
-Size=759,2136
+Size=936,1983
-Collapsed=0
-DockId=0x00000010,0
-
-[Window][Files & Media]
-Pos=0,1719
-Size=999,441
-Collapsed=0
-DockId=0x00000006,1
-
-[Window][AI Settings]
-Pos=0,24
-Size=999,1693
 Collapsed=0
 DockId=0x00000005,0
 
+[Window][Files & Media]
+Pos=0,1010
+Size=828,999
+Collapsed=0
+DockId=0x00000002,0
+
+[Window][AI Settings]
+Pos=0,26
+Size=828,982
+Collapsed=0
+DockId=0x00000001,0
+
 [Window][Approve Tool Execution]
 Pos=3,524
 Size=416,325
 Collapsed=0
 
 [Window][MMA Dashboard]
-Pos=2671,24
+Pos=3360,26
-Size=1169,2136
+Size=480,2134
 Collapsed=0
-DockId=0x00000002,0
+DockId=0x00000010,0
 
 [Window][Log Management]
-Pos=1931,24
+Pos=3360,26
-Size=629,1416
+Size=480,2134
 Collapsed=0
-DockId=0x00000002,1
+DockId=0x00000010,0
 
 [Window][Track Proposal]
 Pos=709,326
@@ -166,7 +167,7 @@ Collapsed=0
 Pos=2822,1717
 Size=1018,420
 Collapsed=0
-DockId=0x00000004,0
+DockId=0x0000000C,0
 
 [Window][Approve PowerShell Command]
 Pos=649,435
@@ -174,8 +175,8 @@ Size=381,329
 Collapsed=0
 
 [Window][Last Script Output]
-Pos=2810,265
+Pos=2567,1006
-Size=800,562
+Size=746,548
 Collapsed=0
 
 [Window][Text Viewer - Log Entry #1 (request)]
@@ -189,7 +190,7 @@ Size=1005,366
 Collapsed=0
 
 [Window][Text Viewer - Entry #11]
-Pos=60,60
+Pos=1010,564
 Size=1529,925
 Collapsed=0
 
@@ -209,7 +210,7 @@ Size=3840,32
 Collapsed=0
 
 [Window][Text Viewer - message]
-Pos=562,588
+Pos=568,1226
 Size=900,700
 Collapsed=0
 
@@ -219,13 +220,13 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - text]
-Pos=555,644
+Pos=1297,550
 Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - system]
-Pos=377,705
+Pos=901,1502
-Size=900,340
+Size=876,536
 Collapsed=0
 
 [Window][Text Viewer - Entry #15]
@@ -239,8 +240,8 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - tool_calls]
-Pos=589,490
+Pos=1106,942
-Size=900,700
+Size=831,482
 Collapsed=0
 
 [Window][Text Viewer - Tool Script #1]
@@ -284,7 +285,7 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - Tool Call #1 Details]
-Pos=165,1081
+Pos=963,716
 Size=727,725
 Collapsed=0
 
@@ -329,9 +330,10 @@ Size=967,499
 Collapsed=0
 
 [Window][Usage Analytics]
-Pos=1702,689
+Pos=2678,26
-Size=566,438
+Size=1162,2134
 Collapsed=0
+DockId=0x0000000F,0
 
 [Window][Tool Preset Manager]
 Pos=1301,302
@@ -364,7 +366,7 @@ Size=900,700
 Collapsed=0
 
 [Window][Text Viewer - Entry #4]
-Pos=828,397
+Pos=1165,782
 Size=900,700
 Collapsed=0
 
@@ -374,17 +376,27 @@ 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][Shader Editor]
+[Window][Text Viewer - Entry #2]
-Pos=753,637
+Pos=1518,488
-Size=493,487
-Collapsed=0
-
-[Window][Text Viewer - list_directory]
-Pos=60,60
 Size=900,700
 Collapsed=0
 
@@ -419,11 +431,11 @@ Column 3  Width=20
 Column 4  Weight=1.0000
 
 [Table][0x2A6000B6,4]
-RefScale=16
+RefScale=18
-Column 0  Width=48
+Column 0  Width=54
-Column 1  Width=68
+Column 1  Width=76
 Column 2  Weight=1.0000
-Column 3  Width=120
+Column 3  Width=274
 
 [Table][0x8BCC69C7,6]
 RefScale=13
@@ -435,18 +447,18 @@ Column 4  Weight=1.0000
 Column 5  Width=50
 
 [Table][0x3751446B,4]
-RefScale=16
+RefScale=18
-Column 0  Width=48
+Column 0  Width=54
-Column 1  Width=72
+Column 1  Width=81
 Column 2  Weight=1.0000
-Column 3  Width=120
+Column 3  Width=135
 
 [Table][0x2C515046,4]
-RefScale=16
+RefScale=18
-Column 0  Width=48
+Column 0  Width=54
 Column 1  Weight=1.0000
-Column 2  Width=117
+Column 2  Width=132
-Column 3  Width=48
+Column 3  Width=54
 
 [Table][0xD99F45C5,4]
 Column 0  Sort=0v
@@ -467,9 +479,9 @@ Column 1  Width=100
 Column 2  Weight=1.0000
 
 [Table][0xA02D8C87,3]
-RefScale=16
+RefScale=18
-Column 0  Width=180
+Column 0  Width=202
-Column 1  Width=120
+Column 1  Width=135
 Column 2  Weight=1.0000
 
 [Table][0xD0277E63,2]
@@ -483,13 +495,13 @@ Column 0  Width=150
 Column 1  Weight=1.0000
 
 [Table][0x8D8494AB,2]
-RefScale=16
+RefScale=18
-Column 0  Width=132
+Column 0  Width=148
 Column 1  Weight=1.0000
 
 [Table][0x2C261E6E,2]
-RefScale=16
+RefScale=18
-Column 0  Width=99
+Column 0  Width=111
 Column 1  Weight=1.0000
 
 [Table][0x9CB1E6FD,2]
@@ -501,19 +513,23 @@ Column 1  Weight=1.0000
 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=3840,2136 Split=X
+DockSpace           ID=0xAFC85805 Window=0x079D3A04 Pos=0,26 Size=3031,1983 Split=X
-  DockNode          ID=0x00000003 Parent=0xAFC85805 SizeRef=1617,1183 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=999,858 Split=Y Selected=0x7BD57D6A
+      DockNode      ID=0x00000007 Parent=0x0000000B SizeRef=828,858 Split=Y Selected=0x8CA2375C
-        DockNode    ID=0x00000005 Parent=0x00000007 SizeRef=639,904 CentralNode=1 Selected=0x7BD57D6A
+        DockNode    ID=0x00000001 Parent=0x00000007 SizeRef=824,1056 CentralNode=1 Selected=0x7BD57D6A
-        DockNode    ID=0x00000006 Parent=0x00000007 SizeRef=639,441 Selected=0x1DCB2623
+        DockNode    ID=0x00000002 Parent=0x00000007 SizeRef=824,999 Selected=0xF4139CA2
-      DockNode      ID=0x0000000E Parent=0x0000000B SizeRef=2839,858 Split=X Selected=0x418C7449
+      DockNode      ID=0x0000000E Parent=0x0000000B SizeRef=2201,858 Split=X Selected=0x418C7449
-        DockNode    ID=0x00000001 Parent=0x0000000E SizeRef=1668,1288 Split=X Selected=0x6F2B5B04
+        DockNode    ID=0x00000012 Parent=0x0000000E SizeRef=936,402 Split=Y Selected=0x418C7449
-          DockNode  ID=0x00000010 Parent=0x00000001 SizeRef=759,1416 Selected=0x418C7449
+          DockNode  ID=0x00000005 Parent=0x00000012 SizeRef=876,1749 Selected=0x418C7449
-          DockNode  ID=0x00000011 Parent=0x00000001 SizeRef=907,1416 Selected=0x6F2B5B04
+          DockNode  ID=0x00000006 Parent=0x00000012 SizeRef=876,362 Selected=0x1D56B311
-        DockNode    ID=0x00000002 Parent=0x0000000E SizeRef=1169,1288 Selected=0x8CA2375C
+        DockNode    ID=0x00000013 Parent=0x0000000E SizeRef=1263,402 Selected=0x6F2B5B04
     DockNode        ID=0x0000000D Parent=0x00000003 SizeRef=435,1186 Selected=0x363E93D6
-  DockNode          ID=0x00000004 Parent=0xAFC85805 SizeRef=511,1183 Selected=0x3AEC3498
+  DockNode          ID=0x00000004 Parent=0xAFC85805 SizeRef=1162,1183 Split=Y Selected=0x3AEC3498
+    DockNode        ID=0x00000010 Parent=0x00000004 SizeRef=1199,1689 Selected=0xB4CBF21A
+    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
 
 ;;;<<<Layout_655921752_Default>>>;;;
 ;;;<<<HelloImGui_Misc>>>;;;

mock_debug_prompt.txt

@@ -3096,3 +3096,26 @@ PROMPT:
 role: tool
 Here are the results: {"content": "done"}
 ------------------
+--- MOCK INVOKED ---
+ARGS: ['tests/mock_gemini_cli.py']
+PROMPT:
+PATH: Epic Initialization — please produce tracks
+------------------
+--- MOCK INVOKED ---
+ARGS: ['tests/mock_gemini_cli.py']
+PROMPT:
+Please generate the implementation tickets for this track.
+------------------
+--- MOCK INVOKED ---
+ARGS: ['tests/mock_gemini_cli.py']
+PROMPT:
+Please read test.txt
+You are assigned to Ticket T1.
+Task Description: do something
+------------------
+--- MOCK INVOKED ---
+ARGS: ['tests/mock_gemini_cli.py']
+PROMPT:
+role: tool
+Here are the results: {"content": "done"}
+------------------

project_history.toml

@@ -9,5 +9,5 @@ active = "main"
 
 [discussions.main]
 git_commit = ""
-last_updated = "2026-03-12T20:34:43"
+last_updated = "2026-03-14T09:29:30"
 history = []

src/api_hooks.py

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

src/app_controller.py

@@ -25,6 +25,7 @@ from src import project_manager
 from src import performance_monitor
 from src import models
 from src import presets
+from src import thinking_parser
 from src.file_cache import ASTParser
 from src import ai_client
 from src import shell_runner
@@ -242,6 +243,8 @@ class AppController:
   self.ai_status: str = 'idle'
   self.ai_response: str = ''
   self.last_md: str = ''
+  self.last_aggregate_markdown: str = ''
+  self.last_resolved_system_prompt: str = ''
   self.last_md_path: Optional[Path] = None
   self.last_file_items: List[Any] = []
   self.send_thread: Optional[threading.Thread] = None
@@ -251,6 +254,7 @@ class AppController:
   self.show_text_viewer: bool = False
   self.text_viewer_title: str = ''
   self.text_viewer_content: str = ''
+  self.text_viewer_type: str = 'text'
   self._pending_comms: List[Dict[str, Any]] = []
   self._pending_tool_calls: List[Dict[str, Any]] = []
   self._pending_history_adds: List[Dict[str, Any]] = []
@@ -374,7 +378,10 @@ class AppController:
    'ui_separate_tier1': 'ui_separate_tier1',
    'ui_separate_tier2': 'ui_separate_tier2',
    'ui_separate_tier3': 'ui_separate_tier3',
-   'ui_separate_tier4': 'ui_separate_tier4'
+   'ui_separate_tier4': 'ui_separate_tier4',
+   'show_text_viewer': 'show_text_viewer',
+   'text_viewer_title': 'text_viewer_title',
+   'text_viewer_type': 'text_viewer_type'
   }
   self._gettable_fields = dict(self._settable_fields)
   self._gettable_fields.update({
@@ -421,7 +428,10 @@ class AppController:
    'ui_separate_tier1': 'ui_separate_tier1',
    'ui_separate_tier2': 'ui_separate_tier2',
    'ui_separate_tier3': 'ui_separate_tier3',
-   'ui_separate_tier4': 'ui_separate_tier4'
+   'ui_separate_tier4': 'ui_separate_tier4',
+   'show_text_viewer': 'show_text_viewer',
+   'text_viewer_title': 'text_viewer_title',
+   'text_viewer_type': 'text_viewer_type'
   })
   self.perf_monitor = performance_monitor.get_monitor()
   self._perf_profiling_enabled = False
@@ -610,16 +620,6 @@ 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")
@@ -1467,9 +1467,22 @@ 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"]:
+   inp = u.get("input_tokens", u.get("prompt_tokens", 0))
-    if k in u:
+   out = u.get("output_tokens", u.get("completion_tokens", 0))
-     self.session_usage[k] += u.get(k, 0) or 0
+   cache_read = u.get("cache_read_input_tokens", 0)
+   cache_create = u.get("cache_creation_input_tokens", 0)
+   total = u.get("total_tokens", 0)
+
+   # Store normalized usage back in payload for history rendering
+   u["input_tokens"] = inp
+   u["output_tokens"] = out
+   u["cache_read_input_tokens"] = cache_read
+
+   self.session_usage["input_tokens"] += inp
+   self.session_usage["output_tokens"] += out
+   self.session_usage["cache_read_input_tokens"] += cache_read
+   self.session_usage["cache_creation_input_tokens"] += cache_create
+   self.session_usage["total_tokens"] += total
    input_t = u.get("input_tokens", 0)
    output_t = u.get("output_tokens", 0)
    model = payload.get("model", "unknown")
@@ -1490,22 +1503,42 @@ class AppController:
       "ts": entry.get("ts", project_manager.now_ts())
      })
 
-  if kind in ("tool_result", "tool_call"):
+  if kind == "response":
-   role = "Tool" if kind == "tool_result" else "Vendor API"
+   if self.ui_auto_add_history:
-   content = ""
+    role = payload.get("role", "AI")
-   if kind == "tool_result":
+    text_content = payload.get("text", "")
-    content = payload.get("output", "")
+    if text_content.strip():
-   else:
+     segments, parsed_response = thinking_parser.parse_thinking_trace(text_content)
-    content = payload.get("script") or payload.get("args") or payload.get("message", "")
+     entry_obj = {
-    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}",
+      "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:
@@ -2485,6 +2518,11 @@ class AppController:
   # Build discussion history text separately
   history = flat.get("discussion", {}).get("history", [])
   discussion_text = aggregate.build_discussion_text(history)
+  
+  csp = filter(bool, [self.ui_global_system_prompt.strip(), self.ui_project_system_prompt.strip()])
+  self.last_resolved_system_prompt = "\n\n".join(csp)
+  self.last_aggregate_markdown = full_md
+  
   return full_md, path, file_items, stable_md, discussion_text
 
  def _cb_plan_epic(self) -> None:

src/models.py

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

src/project_manager.py

@@ -33,6 +33,14 @@ def entry_to_str(entry: dict[str, Any]) -> str:
  ts = entry.get("ts", "")
  role = entry.get("role", "User")
  content = entry.get("content", "")
+ 
+ segments = entry.get("thinking_segments")
+ if segments:
+  for s in segments:
+   marker = s.get("marker", "thinking")
+   s_content = s.get("content", "")
+   content = f"<{marker}>\n{s_content}\n</{marker}>\n{content}"
+   
  if ts:
   return f"@{ts}\n{role}:\n{content}"
  return f"{role}:\n{content}"
@@ -93,6 +101,7 @@ def default_project(name: str = "unnamed") -> dict[str, Any]:
   "output":      {"output_dir": "./md_gen"},
   "files":       {"base_dir": ".", "paths": [], "tier_assignments": {}},
   "screenshots": {"base_dir": ".", "paths": []},
+  "context_presets": {},
   "gemini_cli":  {"binary_path": "gemini"},
   "deepseek":    {"reasoning_effort": "medium"},
   "agent":       {
@@ -231,15 +240,37 @@ def flat_config(proj: dict[str, Any], disc_name: Optional[str] = None, track_id:
   disc_data = disc_sec.get("discussions", {}).get(name, {})
   history = disc_data.get("history", [])
  return {
-  "project":     proj.get("project", {}),
+  "project":         proj.get("project", {}),
-  "output":      proj.get("output", {}),
+  "output":          proj.get("output", {}),
-  "files":       proj.get("files",  {}),
+  "files":           proj.get("files",  {}),
-  "screenshots": proj.get("screenshots", {}),
+  "screenshots":     proj.get("screenshots", {}),
-  "discussion":  {
+  "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:

src/shader_manager.py

@@ -5,113 +5,6 @@ class ShaderManager:
   self.program = None
   self.bg_program = None
   self.pp_program = None
-  self.blur_h_program = None
-  self.blur_v_program = None
-  self.blur_fbo = None
-  self.scene_fbo = None
-  self.temp_fbo = None
-  self.scene_tex = None
-  self.blur_tex = None
-  self.temp_tex = None
-  self.fbo_width = 0
-  self.fbo_height = 0
-  self._vao = None
-
- def _ensure_vao(self):
-  if self._vao is None:
-   try:
-    import sys
-    if sys.platform == "win32":
-     self._vao = gl.glGenVertexArrays(1)
-    else:
-     # Some non-win32 environments might not support VAOs or need different handling
-     self._vao = gl.glGenVertexArrays(1)
-   except Exception:
-    pass
-  if self._vao is not None:
-   gl.glBindVertexArray(self._vao)
-
- def setup_capture_fbo(self, width, height):
-  if self.blur_fbo is not None:
-   gl.glDeleteFramebuffers(1, [self.blur_fbo])
-  if self.scene_fbo is not None:
-   gl.glDeleteFramebuffers(1, [self.scene_fbo])
-  if self.temp_fbo is not None:
-   gl.glDeleteFramebuffers(1, [self.temp_fbo])
-  if self.scene_tex is not None:
-   gl.glDeleteTextures(1, [self.scene_tex])
-  if self.blur_tex is not None:
-   gl.glDeleteTextures(1, [self.blur_tex])
-  if self.temp_tex is not None:
-   gl.glDeleteTextures(1, [self.temp_tex])
-  
-  self.scene_tex = gl.glGenTextures(1)
-  gl.glBindTexture(gl.GL_TEXTURE_2D, self.scene_tex)
-  gl.glTexImage2D(gl.GL_TEXTURE_2D, 0, gl.GL_RGBA, width, height, 0, gl.GL_RGBA, gl.GL_UNSIGNED_BYTE, None)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MIN_FILTER, gl.GL_LINEAR)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MAG_FILTER, gl.GL_LINEAR)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_WRAP_S, gl.GL_CLAMP_TO_EDGE)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_WRAP_T, gl.GL_CLAMP_TO_EDGE)
-  
-  self.scene_fbo = gl.glGenFramebuffers(1)
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self.scene_fbo)
-  gl.glFramebufferTexture2D(gl.GL_FRAMEBUFFER, gl.GL_COLOR_ATTACHMENT0, gl.GL_TEXTURE_2D, self.scene_tex, 0)
-  if gl.glCheckFramebufferStatus(gl.GL_FRAMEBUFFER) != gl.GL_FRAMEBUFFER_COMPLETE:
-   raise RuntimeError("Scene Framebuffer not complete")
-
-  self.temp_tex = gl.glGenTextures(1)
-  gl.glBindTexture(gl.GL_TEXTURE_2D, self.temp_tex)
-  gl.glTexImage2D(gl.GL_TEXTURE_2D, 0, gl.GL_RGBA, width, height, 0, gl.GL_RGBA, gl.GL_UNSIGNED_BYTE, None)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MIN_FILTER, gl.GL_LINEAR)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MAG_FILTER, gl.GL_LINEAR)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_WRAP_S, gl.GL_CLAMP_TO_EDGE)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_WRAP_T, gl.GL_CLAMP_TO_EDGE)
-
-  self.temp_fbo = gl.glGenFramebuffers(1)
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self.temp_fbo)
-  gl.glFramebufferTexture2D(gl.GL_FRAMEBUFFER, gl.GL_COLOR_ATTACHMENT0, gl.GL_TEXTURE_2D, self.temp_tex, 0)
-  if gl.glCheckFramebufferStatus(gl.GL_FRAMEBUFFER) != gl.GL_FRAMEBUFFER_COMPLETE:
-   raise RuntimeError("Temp Framebuffer not complete")
-
-  self.blur_tex = gl.glGenTextures(1)
-  gl.glBindTexture(gl.GL_TEXTURE_2D, self.blur_tex)
-  gl.glTexImage2D(gl.GL_TEXTURE_2D, 0, gl.GL_RGBA, width, height, 0, gl.GL_RGBA, gl.GL_UNSIGNED_BYTE, None)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MIN_FILTER, gl.GL_LINEAR)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_MAG_FILTER, gl.GL_LINEAR)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_WRAP_S, gl.GL_CLAMP_TO_EDGE)
-  gl.glTexParameteri(gl.GL_TEXTURE_2D, gl.GL_TEXTURE_WRAP_T, gl.GL_CLAMP_TO_EDGE)
-
-  self.blur_fbo = gl.glGenFramebuffers(1)
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self.blur_fbo)
-  gl.glFramebufferTexture2D(gl.GL_FRAMEBUFFER, gl.GL_COLOR_ATTACHMENT0, gl.GL_TEXTURE_2D, self.blur_tex, 0)
-  if gl.glCheckFramebufferStatus(gl.GL_FRAMEBUFFER) != gl.GL_FRAMEBUFFER_COMPLETE:
-   raise RuntimeError("Blur Framebuffer not complete")
-
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, 0)
-  self.fbo_width = width
-  self.fbo_height = height
-
- def render_background_to_fbo(self, width, height, time):
-  if self.scene_fbo is None or self.fbo_width != width or self.fbo_height != height:
-   self.setup_capture_fbo(width, height)
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self.scene_fbo)
-  gl.glViewport(0, 0, width, height)
-  self.render_background(width, height, time)
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, 0)
-
- def prepare_global_blur(self, width, height, radius, tint, opacity, time):
-  self.render_background_to_fbo(width, height, time)
-  self.render_blur(self.scene_tex, width, height, radius, tint, opacity)
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, 0)
-
- def capture_begin(self, width, height):
-  if self.blur_fbo is None or self.fbo_width != width or self.fbo_height != height:
-   self.setup_capture_fbo(width, height)
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self.blur_fbo)
-  gl.glViewport(0, 0, width, height)
-
- def capture_end(self):
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, 0)
 
  def compile_shader(self, vertex_src: str, fragment_src: str) -> int:
   program = gl.glCreateProgram()
@@ -186,44 +79,9 @@ void main() {
 uniform float u_time;
 uniform vec2 u_resolution;
 out vec4 FragColor;
-
-float hash(vec2 p) {
- return fract(sin(dot(p, vec2(127.1, 311.7))) * 43758.5453123);
-}
-
-float noise(vec2 p) {
- vec2 i = floor(p);
- vec2 f = fract(p);
- vec2 u = f * f * (3.0 - 2.0 * f);
- return mix(mix(hash(i + vec2(0.0, 0.0)), hash(i + vec2(1.0, 0.0)), u.x),
-      mix(hash(i + vec2(0.0, 1.0)), hash(i + vec2(1.0, 1.0)), u.x), u.y);
-}
-
 void main() {
  vec2 uv = gl_FragCoord.xy / u_resolution.xy;
- vec2 p = uv * 2.0 - 1.0;
+ vec3 col = 0.5 + 0.5 * cos(u_time + uv.xyx + vec3(0, 2, 4));
- p.x *= u_resolution.x / u_resolution.y;
- 
- // Deep sea background gradient (dark blue)
- vec3 col = mix(vec3(0.01, 0.03, 0.08), vec3(0.0, 0.08, 0.15), uv.y);
- 
- // Moving blobs / caustics
- float n = 0.0;
- float t = u_time * 0.15;
- n += noise(p * 1.2 + vec2(t * 0.8, t * 0.5)) * 0.4;
- n += noise(p * 2.5 - vec2(t * 0.4, t * 0.9)) * 0.2;
- 
- col += vec3(0.05, 0.12, 0.22) * n;
- 
- // Bright highlights (caustics approximation)
- float c = 0.0;
- for(int i=0; i<3; i++) {
-  vec2 p2 = p * (float(i) + 1.0) * 0.4;
-  p2 += vec2(sin(t + p2.y * 1.5), cos(t + p2.x * 1.5));
-  c += abs(0.015 / (length(p2) - 0.4));
- }
- col += vec3(0.1, 0.25, 0.45) * c * 0.12;
- 
  FragColor = vec4(col, 1.0);
 }
 """
@@ -239,7 +97,6 @@ void main() {
   u_res_loc = gl.glGetUniformLocation(self.bg_program, "u_resolution")
   if u_res_loc != -1:
    gl.glUniform2f(u_res_loc, float(width), float(height))
-  self._ensure_vao()
   gl.glDrawArrays(gl.GL_TRIANGLE_STRIP, 0, 4)
   gl.glUseProgram(0)
 
@@ -291,114 +148,6 @@ void main() {
   u_time_loc = gl.glGetUniformLocation(self.pp_program, "u_time")
   if u_time_loc != -1:
    gl.glUniform1f(u_time_loc, float(time))
-  self._ensure_vao()
   gl.glDrawArrays(gl.GL_TRIANGLE_STRIP, 0, 4)
   gl.glBindTexture(gl.GL_TEXTURE_2D, 0)
   gl.glUseProgram(0)
-
- def setup_frosted_glass_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_h = """
-#version 330 core
-in vec2 v_uv;
-uniform sampler2D u_texture;
-uniform float u_blur_radius;
-uniform vec2 u_direction;
-out vec4 FragColor;
-void main() {
- float weight[5] = float[](0.227027, 0.1945946, 0.1216216, 0.054054, 0.016216);
- vec2 res = vec2(textureSize(u_texture, 0));
- vec2 tex_offset = (u_blur_radius / res) * u_direction * 2.5; // Multiplied by 2.5 for milky effect
- vec4 result = texture(u_texture, v_uv) * weight[0];
- for(int i = 1; i < 5; ++i) {
-  result += texture(u_texture, v_uv + tex_offset * float(i)) * weight[i];
-  result += texture(u_texture, v_uv - tex_offset * float(i)) * weight[i];
- }
- FragColor = result;
-}
-"""
-  fragment_src_v = """
-#version 330 core
-in vec2 v_uv;
-uniform sampler2D u_texture;
-uniform float u_blur_radius;
-uniform vec2 u_direction;
-uniform float u_tint_intensity;
-uniform float u_opacity;
-out vec4 FragColor;
-void main() {
- float weight[5] = float[](0.227027, 0.1945946, 0.1216216, 0.054054, 0.016216);
- vec2 res = vec2(textureSize(u_texture, 0));
- vec2 tex_offset = (u_blur_radius / res) * u_direction * 2.5; // Multiplied by 2.5 for milky effect
- vec4 result = texture(u_texture, v_uv) * weight[0];
- for(int i = 1; i < 5; ++i) {
-  result += texture(u_texture, v_uv + tex_offset * float(i)) * weight[i];
-  result += texture(u_texture, v_uv - tex_offset * float(i)) * weight[i];
- }
- vec3 tint_color = vec3(0.05, 0.07, 0.12); // Slightly deeper tint
- vec3 tinted = mix(result.rgb, tint_color, u_tint_intensity);
- FragColor = vec4(tinted, result.a * u_opacity);
-}
-"""
-  self.blur_h_program = self.compile_shader(vertex_src, fragment_src_h)
-  self.blur_v_program = self.compile_shader(vertex_src, fragment_src_v)
-
- def render_blur(self, texture_id, width, height, radius, tint, opacity):
-  if not self.blur_h_program or not self.blur_v_program:
-   return
-
-  self._ensure_vao()
-
-  # Pass 1: Horizontal blur to temp_fbo
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self.temp_fbo)
-  gl.glViewport(0, 0, width, height)
-  gl.glClear(gl.GL_COLOR_BUFFER_BIT)
-  
-  gl.glUseProgram(self.blur_h_program)
-  gl.glActiveTexture(gl.GL_TEXTURE0)
-  gl.glBindTexture(gl.GL_TEXTURE_2D, texture_id)
-  
-  gl.glUniform1i(gl.glGetUniformLocation(self.blur_h_program, "u_texture"), 0)
-  gl.glUniform1f(gl.glGetUniformLocation(self.blur_h_program, "u_blur_radius"), float(radius))
-  gl.glUniform2f(gl.glGetUniformLocation(self.blur_h_program, "u_direction"), 1.0, 0.0)
-  
-  gl.glDrawArrays(gl.GL_TRIANGLE_STRIP, 0, 4)
-
-  # Pass 2: Vertical blur to blur_fbo
-  gl.glBindFramebuffer(gl.GL_FRAMEBUFFER, self.blur_fbo)
-  gl.glViewport(0, 0, width, height)
-  gl.glClear(gl.GL_COLOR_BUFFER_BIT)
-  
-  gl.glUseProgram(self.blur_v_program)
-  gl.glActiveTexture(gl.GL_TEXTURE0)
-  gl.glBindTexture(gl.GL_TEXTURE_2D, self.temp_tex)
-  
-  gl.glUniform1i(gl.glGetUniformLocation(self.blur_v_program, "u_texture"), 0)
-  gl.glUniform1f(gl.glGetUniformLocation(self.blur_v_program, "u_blur_radius"), float(radius))
-  gl.glUniform2f(gl.glGetUniformLocation(self.blur_v_program, "u_direction"), 0.0, 1.0)
-  gl.glUniform1f(gl.glGetUniformLocation(self.blur_v_program, "u_tint_intensity"), float(tint))
-  gl.glUniform1f(gl.glGetUniformLocation(self.blur_v_program, "u_opacity"), float(opacity))
-  
-  gl.glDrawArrays(gl.GL_TRIANGLE_STRIP, 0, 4)
-  
-  gl.glBindTexture(gl.GL_TEXTURE_2D, 0)
-  gl.glUseProgram(0)

src/theme_2.py

@@ -235,10 +235,6 @@ _current_font_size: float = 16.0
 _current_scale: float = 1.0
 _transparency: float = 1.0
 _child_transparency: float = 1.0
-_frosted_glass_enabled: bool = False
-_frosted_blur_radius: float = 8.0
-_frosted_tint_intensity: float = 0.1
-_frosted_opacity: float = 1.0
 
 # ------------------------------------------------------------------ public API
 
@@ -273,34 +269,6 @@ def set_child_transparency(val: float) -> None:
  _child_transparency = val
  apply(_current_palette)
 
-def get_frosted_glass_enabled() -> bool:
- return _frosted_glass_enabled
-
-def set_frosted_glass_enabled(val: bool) -> None:
- global _frosted_glass_enabled
- _frosted_glass_enabled = val
-
-def get_frosted_blur_radius() -> float:
- return _frosted_blur_radius
-
-def set_frosted_blur_radius(val: float) -> None:
- global _frosted_blur_radius
- _frosted_blur_radius = val
-
-def get_frosted_tint_intensity() -> float:
- return _frosted_tint_intensity
-
-def set_frosted_tint_intensity(val: float) -> None:
- global _frosted_tint_intensity
- _frosted_tint_intensity = val
-
-def get_frosted_opacity() -> float:
- return _frosted_opacity
-
-def set_frosted_opacity(val: float) -> None:
- global _frosted_opacity
- _frosted_opacity = val
-
 def apply(palette_name: str) -> None:
  """
     Apply a named palette by setting all ImGui style colors and applying global professional styling.
@@ -382,17 +350,13 @@ def save_to_config(config: dict) -> None:
  config["theme"]["scale"] = _current_scale
  config["theme"]["transparency"] = _transparency
  config["theme"]["child_transparency"] = _child_transparency
- config["theme"]["frosted_glass_enabled"] = _frosted_glass_enabled
- config["theme"]["frosted_blur_radius"] = _frosted_blur_radius
- config["theme"]["frosted_tint_intensity"] = _frosted_tint_intensity
- config["theme"]["frosted_opacity"] = _frosted_opacity
  sys.stderr.write(f"[DEBUG theme_2] save_to_config: palette={_current_palette}, transparency={_transparency}\n")
  sys.stderr.flush()
 
 def load_from_config(config: dict) -> None:
  """Read [theme] from config. Font is handled separately at startup."""
  import sys
- global _current_font_path, _current_font_size, _current_scale, _current_palette, _transparency, _child_transparency, _frosted_glass_enabled, _frosted_blur_radius, _frosted_tint_intensity, _frosted_opacity
+ global _current_font_path, _current_font_size, _current_scale, _current_palette, _transparency, _child_transparency
  t = config.get("theme", {})
  sys.stderr.write(f"[DEBUG theme_2] load_from_config raw: {t}\n")
  sys.stderr.flush()
@@ -405,10 +369,6 @@ def load_from_config(config: dict) -> None:
  _current_scale = float(t.get("scale", 1.0))
  _transparency = float(t.get("transparency", 1.0))
  _child_transparency = float(t.get("child_transparency", 1.0))
- _frosted_glass_enabled = bool(t.get("frosted_glass_enabled", False))
- _frosted_blur_radius = float(t.get("frosted_blur_radius", 8.0))
- _frosted_tint_intensity = float(t.get("frosted_tint_intensity", 0.1))
- _frosted_opacity = float(t.get("frosted_opacity", 1.0))
  sys.stderr.write(f"[DEBUG theme_2] load_from_config effective: palette={_current_palette}, transparency={_transparency}\n")
  sys.stderr.flush()
 

src/thinking_parser.py

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

tests/test_context_presets.py

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

tests/test_fbo_capture.py

@@ -1,42 +0,0 @@
-import pytest
-from unittest.mock import patch, MagicMock
-import OpenGL.GL as gl
-
-def test_shader_manager_fbo_initialization():
- with patch("src.shader_manager.gl") as mock_gl:
-  mock_gl.glGenFramebuffers.side_effect = [1, 2]
-  mock_gl.glGenTextures.side_effect = [3, 4]
-  mock_gl.glCheckFramebufferStatus.return_value = mock_gl.GL_FRAMEBUFFER_COMPLETE
-  
-  from src.shader_manager import ShaderManager
-  manager = ShaderManager()
-  
-  manager.setup_capture_fbo(800, 600)
-  
-  assert manager.scene_fbo == 1
-  assert manager.blur_fbo == 2
-  assert manager.scene_tex == 3
-  assert manager.blur_tex == 4
-  assert mock_gl.glGenFramebuffers.call_count == 2
-  assert mock_gl.glGenTextures.call_count == 2
-  assert mock_gl.glCheckFramebufferStatus.call_count == 2
-
-def test_shader_manager_capture_lifecycle():
- with patch("src.shader_manager.gl") as mock_gl:
-  mock_gl.glCheckFramebufferStatus.return_value = mock_gl.GL_FRAMEBUFFER_COMPLETE
-  mock_gl.glGenFramebuffers.side_effect = [1, 2]
-  mock_gl.glGenTextures.side_effect = [3, 4]
-  from src.shader_manager import ShaderManager
-  manager = ShaderManager()
-  
-  # Ensure setup is called on first capture
-  manager.capture_begin(1024, 768)
-  assert manager.fbo_width == 1024
-  assert manager.fbo_height == 768
-  # Should bind the blur FBO
-  mock_gl.glBindFramebuffer.assert_any_call(mock_gl.GL_FRAMEBUFFER, manager.blur_fbo)
-  
-  mock_gl.glBindFramebuffer.reset_mock()
-  manager.capture_end()
-  # Verify unbind (glBindFramebuffer(..., 0))
-  mock_gl.glBindFramebuffer.assert_called_with(mock_gl.GL_FRAMEBUFFER, 0)

tests/test_frosted_glass_shader.py

@@ -1,19 +0,0 @@
-import pytest
-from unittest.mock import patch, MagicMock
-
-def test_shader_manager_frosted_glass_compilation():
- # Mock OpenGL before importing ShaderManager
- with patch("src.shader_manager.gl") as mock_gl:
-  mock_gl.glCreateProgram.return_value = 1
-  mock_gl.glCreateShader.return_value = 2
-  mock_gl.glGetShaderiv.return_value = mock_gl.GL_TRUE
-  mock_gl.glGetProgramiv.return_value = mock_gl.GL_TRUE
-  
-  from src.shader_manager import ShaderManager
-  manager = ShaderManager()
-  
-  # This should fail initially because the method doesn't exist
-  manager.setup_frosted_glass_shader()
-  
-  assert manager.blur_program is not None
-  assert mock_gl.glCreateProgram.called

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_frosted_integration.py

@@ -1,89 +0,0 @@
-import pytest
-import time
-from unittest.mock import patch, MagicMock
-
-def test_gui_frosted_background_call():
- # Mock ShaderManager and OpenGL functions
- with patch("src.gui_2.ShaderManager") as mock_sm_class, \
-      patch("src.gui_2.gl") as mock_gl, \
-      patch("src.gui_2.imgui") as mock_imgui, \
-      patch("src.gui_2.theme") as mock_theme:
-  
-  mock_sm = mock_sm_class.return_value
-  mock_sm.blur_tex = 2
-  mock_theme.get_frosted_glass_enabled.return_value = True
-  
-  mock_imgui.get_io().display_size = MagicMock(x=1920, y=1080)
-  
-  from src.gui_2 import App
-  with patch.object(App, '__init__', return_value=None):
-   app = App()
-   app.shader_manager = mock_sm
-   
-   # Simulate frame
-   app._render_frosted_background(pos=MagicMock(x=10, y=10), size=MagicMock(x=100, y=100))
-   
-   # Now it should only call add_image
-   assert mock_imgui.get_window_draw_list().add_image.called
-   # It no longer calls these
-   assert not mock_sm.setup_capture_fbo.called
-   assert not mock_sm.render_blur.called
-   assert not mock_sm.capture_begin.called
-   assert not mock_sm.capture_end.called
-
-def test_gui_global_blur_call():
- with patch("src.gui_2.ShaderManager") as mock_sm_class, \
-      patch("src.gui_2.imgui") as mock_imgui, \
-      patch("src.gui_2.theme") as mock_theme, \
-      patch("src.gui_2.bg_shader") as mock_bg:
-  
-  mock_sm = mock_sm_class.return_value
-  mock_theme.get_frosted_glass_enabled.return_value = True
-  mock_theme.is_nerv_active.return_value = False
-  mock_imgui.get_io().display_size = MagicMock(x=1920, y=1080)
-  mock_bg.get_bg.return_value = MagicMock(enabled=False)
-  
-  from src.gui_2 import App
-  with patch.object(App, '__init__', return_value=None):
-   app = App()
-   app.shader_manager = mock_sm
-   app.shader_uniforms = {
-    'frosted_blur_radius': 10.0,
-    'frosted_tint_intensity': 0.5,
-    'frosted_opacity': 0.8
-   }
-   app.ai_status = "idle"
-   app.ui_crt_filter = False
-   app.controller = MagicMock()
-   app.perf_profiling_enabled = False
-   app.is_viewing_prior_session = False
-   app.config = {}
-   app.project = {}
-   app.show_windows = {}
-   app.ui_auto_scroll_comms = False
-   app._comms_log_dirty = False
-   app._tool_log_dirty = False
-   app._pending_comms_lock = MagicMock()
-   app._pending_comms = []
-   app.ui_focus_agent = None
-   app._last_ui_focus_agent = None
-   app.perf_monitor = MagicMock()
-   app._process_pending_gui_tasks = MagicMock()
-   app._process_pending_history_adds = MagicMock()
-   app._render_track_proposal_modal = MagicMock()
-   app._render_patch_modal = MagicMock()
-   app._render_save_preset_modal = MagicMock()
-   app._render_preset_manager_window = MagicMock()
-   app._render_tool_preset_manager_window = MagicMock()
-   app._render_persona_editor_window = MagicMock()
-   app._last_autosave = time.time()
-   app._autosave_interval = 60
-   app._render_custom_title_bar = MagicMock()
-   app._render_shader_live_editor = MagicMock()
-   
-   try:
-    app._gui_func()
-   except Exception:
-    pass
-   
-   assert mock_sm.prepare_global_blur.called

tests/test_gui_text_viewer.py

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

tests/test_theme.py

@@ -3,48 +3,33 @@ from unittest.mock import MagicMock
 from src import theme_2 as theme
 
 def test_theme_apply_sets_rounding_and_padding(monkeypatch):
- # Mock imgui
+    # Mock imgui
- mock_style = MagicMock()
+    mock_style = MagicMock()
- mock_imgui = MagicMock()
+    mock_imgui = MagicMock()
- mock_imgui.get_style.return_value = mock_style
+    mock_imgui.get_style.return_value = mock_style
- mock_imgui.ImVec2.side_effect = lambda x, y: (x, y)
+    mock_imgui.ImVec2.side_effect = lambda x, y: (x, y)
- monkeypatch.setattr(theme, "imgui", mock_imgui)
+    monkeypatch.setattr(theme, "imgui", mock_imgui)
 
- # Call apply with the default palette
+    # Call apply with the default palette
- theme.apply("ImGui Dark")
+    theme.apply("ImGui Dark")
 
- # Verify subtle rounding styles
+    # Verify subtle rounding styles
- assert mock_style.window_rounding == 6.0
+    assert mock_style.window_rounding == 6.0
- assert mock_style.child_rounding == 4.0
+    assert mock_style.child_rounding == 4.0
- assert mock_style.frame_rounding == 4.0
+    assert mock_style.frame_rounding == 4.0
- assert mock_style.popup_rounding == 4.0
+    assert mock_style.popup_rounding == 4.0
- assert mock_style.scrollbar_rounding == 12.0
+    assert mock_style.scrollbar_rounding == 12.0
- assert mock_style.grab_rounding == 4.0
+    assert mock_style.grab_rounding == 4.0
- assert mock_style.tab_rounding == 4.0
+    assert mock_style.tab_rounding == 4.0
 
- # Verify borders
+    # Verify borders
- assert mock_style.window_border_size == 1.0
+    assert mock_style.window_border_size == 1.0
- assert mock_style.frame_border_size == 1.0
+    assert mock_style.frame_border_size == 1.0
- assert mock_style.popup_border_size == 1.0
+    assert mock_style.popup_border_size == 1.0
 
- # Verify padding/spacing
+    # Verify padding/spacing
- assert mock_style.window_padding == (8.0, 8.0)
+    assert mock_style.window_padding == (8.0, 8.0)
- assert mock_style.frame_padding == (8.0, 4.0)
+    assert mock_style.frame_padding == (8.0, 4.0)
- assert mock_style.item_spacing == (8.0, 4.0)
+    assert mock_style.item_spacing == (8.0, 4.0)
- assert mock_style.item_inner_spacing == (4.0, 4.0)
+    assert mock_style.item_inner_spacing == (4.0, 4.0)
- assert mock_style.scrollbar_size == 14.0
+    assert mock_style.scrollbar_size == 14.0
-
-def test_frosted_glass_enabled_toggle():
- theme.set_frosted_glass_enabled(True)
- assert theme.get_frosted_glass_enabled() is True
- theme.set_frosted_glass_enabled(False)
- assert theme.get_frosted_glass_enabled() is False
-
-def test_theme_config_frosted_glass():
- config = {"theme": {"frosted_glass_enabled": True}}
- theme.load_from_config(config)
- assert theme.get_frosted_glass_enabled() is True
- 
- new_config = {}
- theme.save_to_config(new_config)
- assert new_config["theme"]["frosted_glass_enabled"] is True

tests/test_thinking_gui.py

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

tests/test_thinking_persistence.py

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

tests/test_thinking_trace.py

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