Reconcile project statuses against Docker on startup, update docs and CI

- Add reconcile_project_statuses command that checks actual Docker container
  state on startup, preserving Running status for containers that are genuinely
  still running and resetting stale statuses to Stopped
- Add is_container_running helper using Docker inspect API
- Frontend calls reconciliation after Docker is confirmed available
- Update TECHNICAL.md project structure, auth modes, and file listings to
  match current codebase
- Update README.md and HOW-TO-USE.md with MCP servers, Mission Control,
  file manager, bash shells, clipboard/audio shims, and progress modal docs
- Add workflow file self-triggers to CI path filters for build-app.yml
  and build.yml
- Install Mission Control skills to ~/.claude/skills/ in entrypoint

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.gitea/workflows/build-app.yml

@@ -10,6 +10,7 @@ on:
     branches: [main]
     paths:
       - "app/**"
+      - ".gitea/workflows/build-app.yml"
   workflow_dispatch:
 
 env:

.gitea/workflows/build.yml

@@ -5,10 +5,12 @@ on:
     branches: [main]
     paths:
       - "container/**"
+      - ".gitea/workflows/build.yml"
   pull_request:
     branches: [main]
     paths:
       - "container/**"
+      - ".gitea/workflows/build.yml"
 
 env:
   REGISTRY: repo.anhonesthost.net

HOW-TO-USE.md

@@ -65,11 +65,11 @@ Switch to the **Projects** tab in the sidebar and click the **+** button.
 
 ### 3. Start the Container
 
-Select your project in the sidebar and click **Start**. The status dot changes from gray (stopped) to orange (starting) to green (running).
+Select your project in the sidebar and click **Start**. A progress modal appears showing real-time status as the container starts. The status dot changes from gray (stopped) to orange (starting) to green (running). The modal auto-closes on success.
 
 ### 4. Open a Terminal
 
-Click the **Terminal** button (highlighted in accent color) to open an interactive terminal session. A new tab appears in the top bar and an xterm.js terminal loads in the main area.
+Click the **Terminal** button to open an interactive terminal session. A new tab appears in the top bar and an xterm.js terminal loads in the main area.
 
 Claude Code launches automatically with `--dangerously-skip-permissions` inside the sandboxed container.
 
@@ -99,16 +99,16 @@ Claude Code launches automatically with `--dangerously-skip-permissions` inside
 │  Sidebar   │                                        │
 │            │          Terminal View                  │
 │  Projects  │         (xterm.js)                     │
+│  MCP       │                                        │
 │  Settings  │                                        │
-│            │                                        │
 ├────────────┴────────────────────────────────────────┤
 │  StatusBar   X projects · X running · X terminals   │
 └─────────────────────────────────────────────────────┘
 ```
 
-- **TopBar** — Terminal tabs for switching between sessions. Status dots on the right show Docker connection (green = connected) and image availability (green = ready).
-- **Sidebar** — Toggle between the **Projects** list and **Settings** panel.
-- **Terminal View** — Interactive terminal powered by xterm.js with WebGL rendering.
+- **TopBar** — Terminal tabs for switching between sessions. Bash shell tabs show a "(bash)" suffix. Status dots on the right show Docker connection (green = connected) and image availability (green = ready).
+- **Sidebar** — Toggle between the **Projects** list, **MCP** server configuration, and **Settings** panel.
+- **Terminal View** — Interactive terminal powered by xterm.js with WebGL rendering. Includes a **Jump to Current** button that appears when you scroll up, so you can quickly return to the latest output.
 - **StatusBar** — Counts of total projects, running containers, and open terminal sessions.
 
 ---
@@ -134,11 +134,17 @@ Select a project in the sidebar to see its action buttons:
 |--------|---------------|--------------|
 | **Start** | Stopped | Creates (if needed) and starts the container |
 | **Stop** | Running | Stops the container but preserves its state |
-| **Terminal** | Running | Opens a new terminal session in this container |
+| **Terminal** | Running | Opens a new Claude Code terminal session |
+| **Shell** | Running | Opens a bash login shell in the container (no Claude Code) |
+| **Files** | Running | Opens the file manager to browse, download, and upload files |
 | **Reset** | Stopped | Destroys and recreates the container from scratch |
 | **Config** | Always | Toggles the configuration panel |
 | **Remove** | Stopped | Deletes the project and its container (with confirmation) |
 
+### Renaming a Project
+
+Double-click the project name in the sidebar to rename it inline. Press **Enter** to confirm or **Escape** to cancel.
+
 ### Container Lifecycle
 
 Containers use a **stop/start** model. When you stop a container, everything inside it is preserved — installed packages, modified files, downloaded tools. Starting it again resumes where you left off.
@@ -147,6 +153,10 @@ Containers use a **stop/start** model. When you stop a container, everything ins
 
 Only **Remove** deletes everything, including the config volume and any stored credentials.
 
+### Container Progress Feedback
+
+When starting, stopping, or resetting a container, a progress modal shows real-time status messages (e.g., "Setting up MCP network...", "Starting MCP containers...", "Creating container..."). If an error occurs, the modal displays the error with a **Close** button. A **Force Stop** option is available if the operation stalls. The modal auto-closes on success.
+
 ---
 
 ## Project Configuration
@@ -177,6 +187,19 @@ When enabled, the host Docker socket is mounted into the container so Claude Cod
 
 > Toggling this requires stopping and restarting the container to take effect.
 
+### Mission Control
+
+Toggle **Mission Control** to integrate [Flight Control](https://github.com/msieurthenardier/mission-control) — an AI-first development methodology — into the project. When enabled:
+
+- The Flight Control repository is automatically cloned into the container
+- Flight Control skills are installed to Claude Code's skill directory (`~/.claude/skills/`)
+- Project instructions are appended with Flight Control workflow guidance
+- The repository is symlinked at `/workspace/mission-control`
+
+Available skills include `/mission`, `/flight`, `/leg`, `/agentic-workflow`, `/flight-debrief`, `/mission-debrief`, `/daily-briefing`, and `/init-project`.
+
+> This setting can only be changed when the container is stopped. Toggling it triggers a container recreation on the next start.
+
 ### Environment Variables
 
 Click **Edit** to open the environment variables modal. Add key-value pairs that will be injected into the container. Per-project variables override global variables with the same key.
@@ -188,8 +211,8 @@ Click **Edit** to open the environment variables modal. Add key-value pairs that
 Click **Edit** to map host ports to container ports. This is useful when Claude Code starts a web server or other service inside the container and you want to access it from your host browser.
 
 Each mapping specifies:
-- **Host Port** — The port on your machine (1–65535)
-- **Container Port** — The port inside the container (1–65535)
+- **Host Port** — The port on your machine (1-65535)
+- **Container Port** — The port inside the container (1-65535)
 - **Protocol** — TCP (default) or UDP
 
 ### Claude Instructions
@@ -198,6 +221,57 @@ Click **Edit** to write per-project instructions for Claude Code. These are writ
 
 ---
 
+## MCP Servers (Beta)
+
+Triple-C supports [Model Context Protocol (MCP)](https://modelcontextprotocol.io/) servers, which extend Claude Code with access to external tools and data sources. MCP servers are configured in a **global library** and **enabled per-project**.
+
+### Accessing MCP Configuration
+
+Click the **MCP** tab in the sidebar to open the MCP server library. This is where you define all available MCP servers.
+
+### Adding an MCP Server
+
+1. Type a name in the input field and click **Add**.
+2. Configure the server in its card:
+
+| Setting | Description |
+|---------|-------------|
+| **Docker Image** | Optional. If provided, the server runs as an isolated Docker container. |
+| **Transport Type** | **Stdio** (command-line) or **HTTP** (network endpoint) |
+
+#### Stdio Mode (Manual)
+- **Command** — The executable to run (e.g., `npx`)
+- **Arguments** — Space-separated arguments
+- **Environment Variables** — Key-value pairs passed to the command
+
+#### HTTP Mode (Manual)
+- **URL** — The MCP endpoint (e.g., `http://localhost:3000/mcp`)
+- **Headers** — Custom HTTP headers
+
+#### Docker Mode
+When a Docker image is specified, the server runs as a container on a per-project network:
+- **Container Port** — Port the MCP server listens on inside its container (default: 3000)
+- **Environment Variables** — Injected into the Docker container
+
+### Enabling MCP Servers Per-Project
+
+In a project's configuration panel, the **MCP Servers** section shows checkboxes for all globally defined servers. Toggle each server on or off for that project. Changes require a container restart.
+
+### How Docker-Based MCP Works
+
+When a project with Docker-based MCP servers starts:
+
+1. A dedicated **bridge network** is created for the project (`triple-c-net-{projectId}`)
+2. Each enabled Docker MCP server gets its own container on that network
+3. The main project container is connected to the same network
+4. MCP server configuration is injected into Claude Code's config file
+
+**Stdio + Docker** servers communicate via `docker exec`, which automatically enables Docker socket access on the main container. **HTTP + Docker** servers are reached by hostname on the shared network (e.g., `http://triple-c-mcp-{serverId}:3000/mcp`).
+
+When MCP configuration changes (servers added/removed/modified), the container is automatically recreated on the next start to apply the new configuration.
+
+---
+
 ## AWS Bedrock Configuration
 
 To use Claude via AWS Bedrock instead of Anthropic's API, switch the auth mode to **Bedrock** on the project card.
@@ -264,7 +338,11 @@ When an update is available, a pulsing **Update** button appears in the top bar.
 
 ### Multiple Sessions
 
-You can open multiple terminal sessions (even for the same project). Each session gets its own tab in the top bar. Click a tab to switch, or click the **x** on a tab to close it.
+You can open multiple terminal sessions (even for the same project). Each session gets its own tab in the top bar. Click a tab to switch, or click the **x** on a tab to close it. Tabs show the project name, with a "(bash)" suffix for shell sessions.
+
+### Bash Shell Sessions
+
+In addition to Claude Code terminals, you can open a plain **bash login shell** in any running container by clicking the **Shell** button. This is useful for manual inspection, package installation, debugging, or running commands that don't need Claude Code.
 
 ### URL Detection
 
@@ -272,9 +350,28 @@ When Claude Code prints a long URL (e.g., during `claude login`), Triple-C detec
 
 Shorter URLs in terminal output are also clickable directly.
 
+### Clipboard Support (OSC 52)
+
+Programs inside the container can copy text to your host clipboard. When a container program uses `xclip`, `xsel`, or `pbcopy`, the text is transparently forwarded to your host clipboard via OSC 52 escape sequences. No additional configuration is required — this works out of the box.
+
 ### Image Paste
 
-You can paste images from your clipboard into the terminal (Ctrl+V / Cmd+V). The image is uploaded to the container and the file path is injected into the terminal input so Claude Code can reference it.
+You can paste images from your clipboard into the terminal (Ctrl+V / Cmd+V). The image is uploaded to the container as `/tmp/clipboard_<timestamp>.png` and the file path is injected into the terminal input so Claude Code can reference it. A toast notification confirms the upload.
+
+### Jump to Current
+
+When you scroll up in the terminal to review previous output, a **Jump to Current** button appears in the bottom-right corner. Click it to scroll back to the latest output.
+
+### File Manager
+
+Click the **Files** button on a running project to open the file manager modal. You can:
+
+- **Browse** the container filesystem starting from `/workspace`, with breadcrumb navigation
+- **Download** any file to your host machine via the download button on each file entry
+- **Upload** files from your host into the current container directory
+- **Refresh** the directory listing at any time
+
+The file manager shows file names, sizes, and modification dates.
 
 ### Terminal Rendering
 
@@ -356,6 +453,8 @@ The sandbox container (Ubuntu 24.04) comes pre-installed with:
 | build-essential | — | C/C++ compiler toolchain |
 | openssh-client | — | SSH for git and remote access |
 
+The container also includes **clipboard shims** (`xclip`, `xsel`, `pbcopy`) that forward copy operations to the host via OSC 52, and an **audio shim** (`rec`, `arecord`) for future voice mode support.
+
 You can install additional tools at runtime with `sudo apt install`, `pip install`, `npm install -g`, etc. Installed packages persist across container stops (but not across resets).
 
 ---
@@ -378,7 +477,7 @@ You can install additional tools at runtime with `sudo apt install`, `pip instal
 
 - Check that the Docker image is "Ready" in Settings.
 - Verify that the mounted folder paths exist on your host.
-- Look at the error message displayed in red below the project card.
+- Look at the error message displayed in the progress modal.
 
 ### OAuth Login URL Not Opening
 
@@ -394,4 +493,10 @@ You can install additional tools at runtime with `sudo apt install`, `pip instal
 ### Settings Won't Save
 
 - Most project settings can only be changed when the container is **stopped**. Stop the container first, make your changes, then start it again.
-- Some changes (like toggling Docker access or changing mounted folders) trigger an automatic container recreation on the next start.
+- Some changes (like toggling Docker access, Mission Control, or changing mounted folders) trigger an automatic container recreation on the next start.
+
+### MCP Containers Not Starting
+
+- Ensure the Docker image for the MCP server exists (pull it first if needed).
+- Check that Docker socket access is available (stdio + Docker MCP servers auto-enable this).
+- Try resetting the project container to force a clean recreation.

README.md

@@ -27,10 +27,10 @@ Triple-C is a cross-platform desktop application that sandboxes Claude Code insi
 ### Container Lifecycle
 
 1. **Create**: New container created with bind mounts, env vars, and labels
-2. **Start**: Container started, entrypoint remaps UID/GID, sets up SSH, configures Docker group
-3. **Terminal**: `docker exec` launches Claude Code with a PTY
-4. **Stop**: Container halted (filesystem persists in named volume)
-5. **Restart**: Existing container restarted; recreated if settings changed (e.g., Docker access toggled)
+2. **Start**: Container started, entrypoint remaps UID/GID, sets up SSH, configures Docker group, sets up MCP servers
+3. **Terminal**: `docker exec` launches Claude Code (or bash shell) with a PTY
+4. **Stop**: Container halted (filesystem persists in named volume); MCP containers stopped
+5. **Restart**: Existing container restarted; recreated if settings changed (detected via SHA-256 fingerprint)
 6. **Reset**: Container removed and recreated from scratch (named volume preserved)
 
 ### Mounts
@@ -41,14 +41,14 @@ Triple-C is a cross-platform desktop application that sandboxes Claude Code insi
 | `/home/claude/.claude` | `triple-c-claude-config-{projectId}` | Named Volume | Persists across container recreation |
 | `/tmp/.host-ssh` | SSH key directory | Bind | Read-only; entrypoint copies to `~/.ssh` |
 | `/home/claude/.aws` | AWS config directory | Bind | Read-only; for Bedrock auth |
-| `/var/run/docker.sock` | Host Docker socket | Bind | Only if "Allow container spawning" is ON |
+| `/var/run/docker.sock` | Host Docker socket | Bind | If "Allow container spawning" is ON, or auto-enabled by stdio+Docker MCP servers |
 
 ### Authentication Modes
 
 Each project can independently use one of:
 
 - **Anthropic** (OAuth): User runs `claude login` inside the terminal on first use. Token persisted in the config volume across restarts and resets.
-- **AWS Bedrock**: Per-project AWS credentials (static keys, profile, or bearer token).
+- **AWS Bedrock**: Per-project AWS credentials (static keys, profile, or bearer token). SSO sessions are validated before launching Claude for Profile auth.
 
 ### Container Spawning (Sibling Containers)
 
@@ -56,6 +56,20 @@ When "Allow container spawning" is enabled per-project, the host Docker socket i
 
 If the Docker access setting is toggled after a container already exists, the container is automatically recreated on next start to apply the mount change. The named config volume (keyed by project ID) is preserved across recreation.
 
+### MCP Server Architecture
+
+Triple-C supports [Model Context Protocol (MCP)](https://modelcontextprotocol.io/) servers as a Beta feature. MCP servers extend Claude Code with external tools and data sources.
+
+- **Global library**: MCP servers are defined globally in the MCP sidebar tab and stored in `mcp_servers.json`
+- **Per-project toggles**: Each project enables/disables individual servers via checkboxes
+- **Docker isolation**: MCP servers can run as isolated Docker containers on a per-project bridge network (`triple-c-net-{projectId}`)
+- **Transport types**: Stdio (command-line) and HTTP (network endpoint), each with manual or Docker mode
+- **Auto-detection**: Config changes are detected via SHA-256 fingerprints and trigger automatic container recreation
+
+### Mission Control Integration
+
+Optional per-project integration with [Flight Control](https://github.com/msieurthenardier/mission-control) — an AI-first development methodology. When enabled, the repo is cloned into the container, skills are installed, and workflow instructions are injected into CLAUDE.md.
+
 ### Docker Socket Path
 
 The socket path is OS-aware:
@@ -75,17 +89,32 @@ Users can override this in Settings via the global `docker_socket_path` option.
 | `app/src/components/layout/StatusBar.tsx` | Running project/terminal counts |
 | `app/src/components/projects/ProjectCard.tsx` | Project config, auth mode, action buttons |
 | `app/src/components/projects/ProjectList.tsx` | Project list in sidebar |
-| `app/src/components/settings/SettingsPanel.tsx` | API key, Docker, AWS settings |
-| `app/src/components/terminal/TerminalView.tsx` | xterm.js terminal with WebGL, URL detection |
-| `app/src/components/terminal/TerminalTabs.tsx` | Tab bar for multiple terminal sessions |
-| `app/src-tauri/src/docker/container.rs` | Container creation, mounts, env vars, inspection |
-| `app/src-tauri/src/docker/exec.rs` | PTY exec sessions for terminal interaction |
+| `app/src/components/projects/FileManagerModal.tsx` | File browser modal (browse, download, upload) |
+| `app/src/components/projects/ContainerProgressModal.tsx` | Real-time container operation progress |
+| `app/src/components/mcp/McpPanel.tsx` | MCP server library (global configuration) |
+| `app/src/components/mcp/McpServerCard.tsx` | Individual MCP server configuration card |
+| `app/src/components/settings/SettingsPanel.tsx` | Docker, AWS, timezone, and global settings |
+| `app/src/components/terminal/TerminalView.tsx` | xterm.js terminal with WebGL, URL detection, OSC 52 clipboard, image paste |
+| `app/src/components/terminal/TerminalTabs.tsx` | Tab bar for multiple terminal sessions (claude + bash) |
+| `app/src/hooks/useTerminal.ts` | Terminal session management (claude and bash modes) |
+| `app/src/hooks/useFileManager.ts` | File manager operations (list, download, upload) |
+| `app/src/hooks/useMcpServers.ts` | MCP server CRUD operations |
+| `app/src/hooks/useVoice.ts` | Voice mode audio capture (currently hidden) |
+| `app/src-tauri/src/docker/container.rs` | Container creation, mounts, env vars, MCP injection, fingerprinting |
+| `app/src-tauri/src/docker/exec.rs` | PTY exec sessions, file upload/download via tar |
 | `app/src-tauri/src/docker/image.rs` | Image building/pulling |
+| `app/src-tauri/src/docker/network.rs` | Per-project bridge networks for MCP containers |
 | `app/src-tauri/src/commands/project_commands.rs` | Start/stop/rebuild Tauri command handlers |
-| `app/src-tauri/src/models/project.rs` | Project struct (auth mode, Docker access, etc.) |
-| `app/src-tauri/src/models/app_settings.rs` | Global settings (image source, Docker socket, AWS) |
-| `container/Dockerfile` | Ubuntu 24.04 sandbox image with Claude Code + dev tools |
-| `container/entrypoint.sh` | UID/GID remap, SSH setup, Docker group config |
+| `app/src-tauri/src/commands/file_commands.rs` | File manager Tauri commands (list, download, upload) |
+| `app/src-tauri/src/commands/mcp_commands.rs` | MCP server CRUD Tauri commands |
+| `app/src-tauri/src/models/project.rs` | Project struct (auth mode, Docker access, MCP servers, Mission Control) |
+| `app/src-tauri/src/models/mcp_server.rs` | MCP server struct (transport, Docker image, env vars) |
+| `app/src-tauri/src/models/app_settings.rs` | Global settings (image source, Docker socket, AWS, microphone) |
+| `app/src-tauri/src/storage/mcp_store.rs` | MCP server persistence (JSON with atomic writes) |
+| `container/Dockerfile` | Ubuntu 24.04 sandbox image with Claude Code + dev tools + clipboard/audio shims |
+| `container/entrypoint.sh` | UID/GID remap, SSH setup, Docker group config, MCP injection, Mission Control setup |
+| `container/osc52-clipboard` | Clipboard shim (xclip/xsel/pbcopy via OSC 52) |
+| `container/audio-shim` | Audio capture shim (rec/arecord via FIFO) for voice mode |
 
 ## CSS / Styling Notes
 
@@ -100,4 +129,6 @@ Users can override this in Settings via the global `docker_socket_path` option.
 
 **Pre-installed tools**: Claude Code, Node.js 22 LTS + pnpm, Python 3.12 + uv + ruff, Rust (stable), Docker CLI, git + gh, AWS CLI v2, ripgrep, openssh-client, build-essential
 
-**Default user**: `claude` (UID/GID 1000, remapped by entrypoint to match host)
+**Shims**: `xclip`/`xsel`/`pbcopy` (OSC 52 clipboard forwarding), `rec`/`arecord` (audio FIFO for voice mode)
+
+**Default user**: `claude` (UID/GID 1000, remapped by entrypoint to match host)

TECHNICAL.md

@@ -154,13 +154,12 @@ The `.claude` configuration directory uses a **named Docker volume** (`triple-c-
 
 ### Authentication Modes
 
-Each project independently chooses one of three authentication methods:
+Each project independently chooses one of two authentication methods:
 
 | Mode | How It Works | When to Use |
 |------|-------------|-------------|
-| **Login (OAuth)** | User runs `claude login` or `/login` inside the terminal. OAuth URL opens in host browser via the web links addon. Token persists in the `.claude` config volume. | Personal use, interactive sessions |
-| **API Key** | Key stored in OS keychain, injected as `ANTHROPIC_API_KEY` env var at container creation. | Automated workflows, team-shared keys |
-| **AWS Bedrock** | Per-project AWS credentials (static, profile, or bearer token) injected as env vars. `~/.aws` config optionally bind-mounted read-only. | Enterprise environments using Bedrock |
+| **Anthropic (OAuth)** | User runs `claude login` or `/login` inside the terminal. OAuth URL opens in host browser via URL detection. Token persists in the `.claude` config volume. | Default — personal and team use |
+| **AWS Bedrock** | Per-project AWS credentials (static keys, profile, or bearer token) injected as env vars. `~/.aws` config optionally bind-mounted read-only. | Enterprise environments using Bedrock |
 
 ### UID/GID Remapping
 
@@ -213,66 +212,93 @@ The `TerminalView` component works around this with a **URL accumulator**:
 
 ```
 triple-c/
-├── LICENSE                     # MIT
-├── TECHNICAL.md                # This document
-├── Triple-C.md                 # Project overview
+├── README.md                      # Architecture overview
+├── TECHNICAL.md                   # This document
+├── HOW-TO-USE.md                  # User guide
+├── BUILDING.md                    # Build instructions
+├── CLAUDE.md                      # Claude Code instructions
 │
 ├── container/
-│   ├── Dockerfile              # Ubuntu 24.04 + all dev tools + Claude Code
-│   └── entrypoint.sh           # UID/GID remap, SSH setup, git config
+│   ├── Dockerfile                 # Ubuntu 24.04 + all dev tools + Claude Code
+│   ├── entrypoint.sh              # UID/GID remap, SSH setup, git config, MCP injection
+│   ├── osc52-clipboard            # Clipboard shim (xclip/xsel/pbcopy via OSC 52)
+│   ├── audio-shim                 # Audio capture shim (rec/arecord via FIFO)
+│   ├── triple-c-scheduler         # Bash-based cron task system
+│   └── triple-c-task-runner       # Task execution runner for scheduler
 │
-└── app/                        # Tauri v2 desktop application
-    ├── package.json            # React, xterm.js, zustand, tailwindcss
-    ├── vite.config.ts          # Vite bundler config
-    ├── index.html              # HTML entry point
+├── .gitea/
+│   └── workflows/
+│       ├── build-app.yml          # Build Tauri app (Linux/macOS/Windows)
+│       ├── build.yml              # Build container image (multi-arch)
+│       ├── sync-release.yml       # Mirror releases to GitHub
+│       └── backfill-releases.yml  # Bulk copy releases to GitHub
+│
+└── app/                           # Tauri v2 desktop application
+    ├── package.json               # React, xterm.js, zustand, tailwindcss
+    ├── vite.config.ts             # Vite bundler config
+    ├── index.html                 # HTML entry point
     │
-    ├── src/                    # React frontend
-    │   ├── main.tsx            # React DOM root
-    │   ├── App.tsx             # Top-level layout
-    │   ├── index.css           # CSS variables, dark theme, scrollbars
+    ├── src/                       # React frontend
+    │   ├── main.tsx               # React DOM root
+    │   ├── App.tsx                # Top-level layout
+    │   ├── index.css              # CSS variables, dark theme, scrollbars
     │   ├── store/
-    │   │   └── appState.ts     # Zustand store (projects, sessions, UI)
+    │   │   └── appState.ts        # Zustand store (projects, sessions, MCP, UI)
     │   ├── hooks/
-    │   │   ├── useDocker.ts    # Docker status, image build
-    │   │   ├── useProjects.ts  # Project CRUD operations
-    │   │   ├── useSettings.ts  # API key, app settings
-    │   │   └── useTerminal.ts  # Terminal I/O, resize, session events
+    │   │   ├── useDocker.ts       # Docker status, image build/pull
+    │   │   ├── useFileManager.ts  # File manager operations
+    │   │   ├── useMcpServers.ts   # MCP server CRUD
+    │   │   ├── useProjects.ts     # Project CRUD operations
+    │   │   ├── useSettings.ts     # App settings
+    │   │   ├── useTerminal.ts     # Terminal I/O, resize, session events
+    │   │   ├── useUpdates.ts      # App update checking
+    │   │   └── useVoice.ts        # Voice mode audio capture
     │   ├── lib/
-    │   │   ├── types.ts        # TypeScript interfaces matching Rust models
-    │   │   ├── tauri-commands.ts # Typed invoke() wrappers
-    │   │   └── constants.ts    # App-wide constants
+    │   │   ├── types.ts           # TypeScript interfaces matching Rust models
+    │   │   ├── tauri-commands.ts  # Typed invoke() wrappers
+    │   │   └── constants.ts       # App-wide constants
     │   └── components/
-    │       ├── layout/         # Sidebar, TopBar, StatusBar
-    │       ├── projects/       # ProjectList, ProjectCard, AddProjectDialog
-    │       ├── terminal/       # TerminalView (xterm.js), TerminalTabs
-    │       ├── settings/       # ApiKeyInput, DockerSettings, AwsSettings
-    │       └── containers/     # SiblingContainers
+    │       ├── layout/            # Sidebar, TopBar, StatusBar
+    │       ├── mcp/               # McpPanel, McpServerCard
+    │       ├── projects/          # ProjectCard, ProjectList, AddProjectDialog,
+    │       │                      # FileManagerModal, ContainerProgressModal, modals
+    │       ├── settings/          # SettingsPanel, DockerSettings, AwsSettings,
+    │       │                      # UpdateDialog
+    │       └── terminal/          # TerminalView (xterm.js), TerminalTabs, UrlToast
     │
-    └── src-tauri/              # Rust backend
-        ├── Cargo.toml          # Rust dependencies
-        ├── tauri.conf.json     # Tauri app configuration
+    └── src-tauri/                 # Rust backend
+        ├── Cargo.toml             # Rust dependencies
+        ├── tauri.conf.json        # Tauri app configuration
         ├── capabilities/
-        │   └── default.json    # Tauri v2 permission grants
+        │   └── default.json       # Tauri v2 permission grants
         └── src/
-            ├── lib.rs          # App builder, plugin + command registration
-            ├── main.rs         # Entry point
-            ├── commands/       # Tauri command handlers
-            │   ├── docker_commands.rs
-            │   ├── project_commands.rs
-            │   ├── settings_commands.rs
-            │   └── terminal_commands.rs
-            ├── docker/         # Docker API layer
-            │   ├── client.rs   # bollard singleton connection
-            │   ├── container.rs # Create, start, stop, remove, inspect
-            │   ├── exec.rs     # PTY exec sessions with bidirectional streaming
-            │   ├── image.rs    # Build from embedded Dockerfile, pull from registry
-            │   └── sibling.rs  # List non-Triple-C containers
-            ├── models/         # Data structures
-            │   ├── project.rs  # Project, AuthMode, BedrockConfig
-            │   └── container_config.rs
-            └── storage/        # Persistence
+            ├── lib.rs             # App builder, plugin + command registration
+            ├── main.rs            # Entry point
+            ├── logging.rs         # Log configuration
+            ├── commands/          # Tauri command handlers
+            │   ├── docker_commands.rs   # Docker status, image ops
+            │   ├── file_commands.rs     # File manager (list/download/upload)
+            │   ├── mcp_commands.rs      # MCP server CRUD
+            │   ├── project_commands.rs  # Start/stop/rebuild containers
+            │   ├── settings_commands.rs # Settings CRUD
+            │   ├── terminal_commands.rs # Terminal I/O, resize
+            │   └── update_commands.rs   # App update checking
+            ├── docker/            # Docker API layer
+            │   ├── client.rs      # bollard singleton connection
+            │   ├── container.rs   # Create, start, stop, remove, fingerprinting
+            │   ├── exec.rs        # PTY exec sessions with bidirectional streaming
+            │   ├── image.rs       # Build from Dockerfile, pull from registry
+            │   └── network.rs     # Per-project bridge networks for MCP
+            ├── models/            # Data structures
+            │   ├── project.rs     # Project, AuthMode, BedrockConfig
+            │   ├── mcp_server.rs  # MCP server configuration
+            │   ├── app_settings.rs # Global settings (image source, AWS, etc.)
+            │   ├── container_config.rs # Image name resolution
+            │   └── update_info.rs # Update metadata
+            └── storage/           # Persistence
                 ├── projects_store.rs  # JSON file with atomic writes
-                ├── settings_store.rs  # App settings
+                ├── mcp_store.rs       # MCP server persistence
+                ├── settings_store.rs  # App settings (Tauri plugin-store)
                 └── secure.rs          # OS keychain via keyring
 ```
 

app/src-tauri/src/commands/project_commands.rs

@@ -386,6 +386,46 @@ pub async fn rebuild_project_container(
     start_project_container(project_id, app_handle, state).await
 }
 
+/// Reconcile project statuses against actual Docker container state.
+/// Called by the frontend after Docker is confirmed available. Projects
+/// marked as Running whose containers are no longer running get reset
+/// to Stopped.
+#[tauri::command]
+pub async fn reconcile_project_statuses(
+    state: State<'_, AppState>,
+) -> Result<Vec<Project>, String> {
+    let projects = state.projects_store.list();
+
+    for project in &projects {
+        if project.status != ProjectStatus::Running && project.status != ProjectStatus::Error {
+            continue;
+        }
+
+        let is_running = if let Some(ref container_id) = project.container_id {
+            docker::is_container_running(container_id).await.unwrap_or(false)
+        } else {
+            false
+        };
+
+        if is_running {
+            log::info!(
+                "Project '{}' ({}) container is still running — keeping Running status",
+                project.name,
+                project.id
+            );
+        } else {
+            log::info!(
+                "Project '{}' ({}) container is not running — setting to Stopped",
+                project.name,
+                project.id
+            );
+            let _ = state.projects_store.update_status(&project.id, ProjectStatus::Stopped);
+        }
+    }
+
+    Ok(state.projects_store.list())
+}
+
 fn default_docker_socket() -> String {
     if cfg!(target_os = "windows") {
         "//./pipe/docker_engine".to_string()

app/src-tauri/src/docker/container.rs

@@ -47,8 +47,8 @@ The `/workspace/mission-control/` directory contains **Flight Control** — an A
 ### How It Works
 
 - **Mission Control is a tool, not a project.** It provides skills and methodology for managing other projects.
-- All Flight Control skills live in `/workspace/mission-control/.claude/skills/`
-- The projects registry at `/workspace/mission-control/projects.md` lists all active projects
+- All Flight Control skills are installed as personal skills in `~/.claude/skills/` and are automatically available as `/slash-commands`
+- The methodology docs and project registry live in `/workspace/mission-control/`
 
 ### When to Use
 
@@ -1031,6 +1031,16 @@ pub async fn get_container_info(project: &Project) -> Result<Option<ContainerInf
     }
 }
 
+/// Check whether a Docker container is currently running.
+/// Returns false if the container doesn't exist or Docker is unavailable.
+pub async fn is_container_running(container_id: &str) -> Result<bool, String> {
+    let docker = get_docker()?;
+    match docker.inspect_container(container_id, None).await {
+        Ok(info) => Ok(info.state.and_then(|s| s.running).unwrap_or(false)),
+        Err(_) => Ok(false),
+    }
+}
+
 pub async fn list_sibling_containers() -> Result<Vec<ContainerSummary>, String> {
     let docker = get_docker()?;
 

app/src-tauri/src/lib.rs

@@ -88,6 +88,7 @@ pub fn run() {
             commands::project_commands::start_project_container,
             commands::project_commands::stop_project_container,
             commands::project_commands::rebuild_project_container,
+            commands::project_commands::reconcile_project_statuses,
             // Settings
             commands::settings_commands::get_settings,
             commands::settings_commands::update_settings,

app/src-tauri/src/storage/projects_store.rs

@@ -72,6 +72,8 @@ impl ProjectsStore {
 
         // Reconcile stale transient statuses: on a cold app start no Docker
         // operations can be in flight, so Starting/Stopping are always stale.
+        // Running/Error are left as-is and reconciled against Docker later
+        // via the reconcile_project_statuses command.
         let mut projects = projects;
         let mut needs_save = needs_save;
         for p in projects.iter_mut() {

app/src/App.tsx

@@ -10,6 +10,7 @@ import { useProjects } from "./hooks/useProjects";
 import { useMcpServers } from "./hooks/useMcpServers";
 import { useUpdates } from "./hooks/useUpdates";
 import { useAppState } from "./store/appState";
+import { reconcileProjectStatuses } from "./lib/tauri-commands";
 
 export default function App() {
   const { checkDocker, checkImage, startDockerPolling } = useDocker();
@@ -17,8 +18,8 @@ export default function App() {
   const { refresh } = useProjects();
   const { refresh: refreshMcp } = useMcpServers();
   const { loadVersion, checkForUpdates, startPeriodicCheck } = useUpdates();
-  const { sessions, activeSessionId } = useAppState(
-    useShallow(s => ({ sessions: s.sessions, activeSessionId: s.activeSessionId }))
+  const { sessions, activeSessionId, setProjects } = useAppState(
+    useShallow(s => ({ sessions: s.sessions, activeSessionId: s.activeSessionId, setProjects: s.setProjects }))
   );
 
   // Initialize on mount
@@ -28,6 +29,14 @@ export default function App() {
     checkDocker().then((available) => {
       if (available) {
         checkImage();
+        // Reconcile project statuses against actual Docker container state,
+        // then refresh the project list so the UI reflects reality.
+        reconcileProjectStatuses().then((projects) => {
+          setProjects(projects);
+        }).catch(() => {
+          // If reconciliation fails (e.g. Docker hiccup), just load from store
+          refresh();
+        });
       } else {
         stopPolling = startDockerPolling();
       }

app/src/lib/tauri-commands.ts

@@ -24,6 +24,8 @@ export const stopProjectContainer = (projectId: string) =>
   invoke<void>("stop_project_container", { projectId });
 export const rebuildProjectContainer = (projectId: string) =>
   invoke<Project>("rebuild_project_container", { projectId });
+export const reconcileProjectStatuses = () =>
+  invoke<Project[]>("reconcile_project_statuses");
 
 // Settings
 export const getSettings = () => invoke<AppSettings>("get_settings");

container/entrypoint.sh

@@ -131,6 +131,15 @@ if [ "$MISSION_CONTROL_ENABLED" = "1" ]; then
     # Symlink into workspace so Claude sees it at /workspace/mission-control
     ln -sfn "$MC_HOME" "$MC_LINK"
     chown -h claude:claude "$MC_LINK"
+
+    # Install skills to ~/.claude/skills/ so Claude Code discovers them automatically
+    if [ -d "$MC_HOME/.claude/skills" ]; then
+        mkdir -p /home/claude/.claude/skills
+        cp -r "$MC_HOME/.claude/skills/"* /home/claude/.claude/skills/ 2>/dev/null
+        chown -R claude:claude /home/claude/.claude/skills
+        echo "entrypoint: mission-control skills installed to ~/.claude/skills/"
+    fi
+
     unset MISSION_CONTROL_ENABLED
 fi