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/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");