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>

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)