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>

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");