fix: stop settings.json from being wiped on launch

Electron main, ssh-manager, and the embedded web server all write the
same settings.json. readJsonFile/readJsonRoot silently coerced any read
failure (including mid-write parse errors) to {}, and writes were plain
fs.writeFile. A partial read during a concurrent write let the reader's
next read-modify-write overwrite the whole file with only the field it
just set — wiping projects, desktopDefaultHostId, and more. Next launch
showed the welcome chooser because defaultHostId was gone, and the
sidebar was empty because projects were gone.

- Switch all writers to atomic tmp+rename so readers never see partial
  JSON.
- Add mutateSettingsRoot() in Electron main to serialize read-modify-
  write pairs across its own call sites (hosts config, window state,
  desktop port, ssh instances, vibrancy).
- Keep read-on-error returning {} to avoid crashing startup callers,
  but log loudly now so we can catch it if it ever happens again.
- useProjectsStore: don't clobber a populated cache with empty incoming
  settings. If settings ever do come back empty, the sidebar stays
  intact until a real, non-empty sync lands.

packages/electron/main.mjs

@@ -295,14 +295,23 @@ const sshManager = new ElectronSshManager({
 const readJsonFile = (filePath) => {
   try {
     return JSON.parse(fs.readFileSync(filePath, 'utf8'));
-  } catch {
+  } catch (error) {
+    if (error && error.code === 'ENOENT') return {};
+    // Parse errors can happen if a concurrent writer just truncated the file
+    // and hasn't finished writing yet. Log loudly so we notice, then return
+    // {} as before. Writes are atomic (tmp + rename) so this race is rare.
+    log.warn?.('[electron] failed to read JSON file', filePath, error);
     return {};
   }
 };
 
 const writeJsonFile = async (filePath, data) => {
   await fsp.mkdir(path.dirname(filePath), { recursive: true });
-  await fsp.writeFile(filePath, JSON.stringify(data, null, 2));
+  // Atomic: write to a temp file then rename. Readers never see a partial
+  // JSON file that could parse-error and get coerced to {}.
+  const tmp = `${filePath}.tmp-${process.pid}-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
+  await fsp.writeFile(tmp, JSON.stringify(data, null, 2));
+  await fsp.rename(tmp, filePath);
 };
 
 const readSettingsRoot = () => {
@@ -310,6 +319,24 @@ const readSettingsRoot = () => {
   return root && typeof root === 'object' && !Array.isArray(root) ? root : {};
 };
 
+// Serializes read-modify-write of the settings file within this process.
+// Multiple call sites (spawnLocalServer, writeDesktopHostsConfig, theme
+// preference saves, ssh manager imports, etc.) would otherwise have their
+// RMW pairs interleave across awaits, letting one writer's stale copy
+// overwrite another writer's just-persisted changes.
+let settingsMutationChain = Promise.resolve();
+const mutateSettingsRoot = (mutator) => {
+  const next = settingsMutationChain.then(async () => {
+    const current = readSettingsRoot();
+    const result = await mutator(current);
+    const nextRoot = result ?? current;
+    await writeJsonFile(settingsFilePath(), nextRoot);
+  });
+  // Keep the chain alive even if one mutator throws.
+  settingsMutationChain = next.catch(() => {});
+  return next;
+};
+
 const writeSettingsRoot = async (root) => writeJsonFile(settingsFilePath(), root);
 
 const normalizeHostUrl = (raw) => {
@@ -350,28 +377,28 @@ const readDesktopHostsConfig = () => {
 };
 
 const writeDesktopHostsConfig = async (config) => {
-  const root = readSettingsRoot();
-  root.desktopHosts = Array.isArray(config?.hosts)
-    ? config.hosts
-        .map((entry) => {
-          const id = typeof entry?.id === 'string' ? entry.id.trim() : '';
-          const url = sanitizeHostUrlForStorage(entry?.url);
-          if (!id || id === LOCAL_HOST_ID || !url) return null;
-          return {
-            id,
-            label: typeof entry?.label === 'string' && entry.label.trim() ? entry.label.trim() : url,
-            url,
-          };
-        })
-        .filter(Boolean)
-    : [];
-  root.desktopDefaultHostId = typeof config?.defaultHostId === 'string' && config.defaultHostId.trim()
-    ? config.defaultHostId.trim()
-    : null;
-  if (typeof config?.initialHostChoiceCompleted === 'boolean') {
-    root.desktopInitialHostChoiceCompleted = config.initialHostChoiceCompleted;
-  }
-  await writeSettingsRoot(root);
+  await mutateSettingsRoot((root) => {
+    root.desktopHosts = Array.isArray(config?.hosts)
+      ? config.hosts
+          .map((entry) => {
+            const id = typeof entry?.id === 'string' ? entry.id.trim() : '';
+            const url = sanitizeHostUrlForStorage(entry?.url);
+            if (!id || id === LOCAL_HOST_ID || !url) return null;
+            return {
+              id,
+              label: typeof entry?.label === 'string' && entry.label.trim() ? entry.label.trim() : url,
+              url,
+            };
+          })
+          .filter(Boolean)
+      : [];
+    root.desktopDefaultHostId = typeof config?.defaultHostId === 'string' && config.defaultHostId.trim()
+      ? config.defaultHostId.trim()
+      : null;
+    if (typeof config?.initialHostChoiceCompleted === 'boolean') {
+      root.desktopInitialHostChoiceCompleted = config.initialHostChoiceCompleted;
+    }
+  });
 };
 
 const readWindowState = () => {
@@ -384,16 +411,16 @@ const writeWindowState = async (browserWindow) => {
   if (!state.mainWindow || browserWindow.id !== state.mainWindow.id) return;
 
   const bounds = browserWindow.getBounds();
-  const root = readSettingsRoot();
-  root.desktopWindowState = {
-    x: bounds.x,
-    y: bounds.y,
-    width: Math.max(bounds.width, MIN_WINDOW_WIDTH),
-    height: Math.max(bounds.height, MIN_WINDOW_HEIGHT),
-    maximized: browserWindow.isMaximized(),
-    fullscreen: browserWindow.isFullScreen(),
-  };
-  await writeSettingsRoot(root);
+  await mutateSettingsRoot((root) => {
+    root.desktopWindowState = {
+      x: bounds.x,
+      y: bounds.y,
+      width: Math.max(bounds.width, MIN_WINDOW_WIDTH),
+      height: Math.max(bounds.height, MIN_WINDOW_HEIGHT),
+      maximized: browserWindow.isMaximized(),
+      fullscreen: browserWindow.isFullScreen(),
+    };
+  });
 };
 
 const debounceWindowStatePersist = (browserWindow, immediate = false) => {
@@ -735,9 +762,9 @@ const spawnLocalServer = async () => {
   state.serverHandle = handle;
   state.sidecarUrl = url;
 
-  const root = readSettingsRoot();
-  root.desktopLocalPort = port;
-  await writeSettingsRoot(root);
+  await mutateSettingsRoot((root) => {
+    root.desktopLocalPort = port;
+  });
 
   return url;
 };
@@ -1445,10 +1472,11 @@ const readDesktopSshInstances = () => {
 };
 
 const writeDesktopSshInstances = async (config) => {
-  const root = readSettingsRoot();
-  root.desktopSshInstances = Array.isArray(config?.instances) ? config.instances : [];
-  await writeSettingsRoot(root);
-  return { instances: root.desktopSshInstances };
+  const nextInstances = Array.isArray(config?.instances) ? config.instances : [];
+  await mutateSettingsRoot((root) => {
+    root.desktopSshInstances = nextInstances;
+  });
+  return { instances: nextInstances };
 };
 
 const updateHostUrlForSshInstance = async (id, label, localUrl) => {
@@ -1783,9 +1811,9 @@ const handleInvoke = async (browserWindow, command, args = {}) => {
       // Tauri build used NSVisualEffectView via Tauri plugin, Electron has
       // no equivalent for our titleBarStyle:'hidden' setup. Persist the
       // disabled state so settings UI reflects it; args.enabled is ignored.
-      const root = readSettingsRoot();
-      root.desktopVibrancy = false;
-      await writeSettingsRoot(root);
+      await mutateSettingsRoot((root) => {
+        root.desktopVibrancy = false;
+      });
       return { enabled: false, requiresRestart: false };
     }
 

packages/electron/ssh-manager.mjs

@@ -72,7 +72,12 @@ const readJsonRoot = (settingsFilePath) => {
 
 const writeJsonRoot = async (settingsFilePath, root) => {
   await fsp.mkdir(path.dirname(settingsFilePath), { recursive: true });
-  await fsp.writeFile(settingsFilePath, JSON.stringify(root, null, 2));
+  // Atomic write: concurrent readers (main.mjs, web server) would otherwise
+  // see partial JSON and readJsonRoot()'s catch would silently coerce to {},
+  // causing the next read-modify-write to wipe the entire settings file.
+  const tmp = `${settingsFilePath}.tmp-${process.pid}-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
+  await fsp.writeFile(tmp, JSON.stringify(root, null, 2));
+  await fsp.rename(tmp, settingsFilePath);
 };
 
 const defaultTrue = () => true;

packages/ui/src/stores/useProjectsStore.ts

@@ -655,6 +655,25 @@ export const useProjectsStore = create<ProjectsStore>()(
         : null;
 
       const current = get();
+
+      // Race guard: settings load can return empty projects during app
+      // rebuild/reinstall or an incomplete settings read. Don't clobber
+      // a populated cache with empty — the sidebar would go blank and
+      // localStorage would be overwritten, losing the list entirely.
+      if (incomingProjects.length === 0 && current.projects.length > 0) {
+        if (incomingActive !== current.activeProjectId) {
+          // Active project may still be valid within the cached list.
+          const activeExists = incomingActive
+            ? current.projects.some((project) => project.id === incomingActive)
+            : true;
+          if (activeExists) {
+            set({ activeProjectId: incomingActive });
+            cacheProjects(current.projects, incomingActive);
+          }
+        }
+        return;
+      }
+
       const projectsChanged = JSON.stringify(current.projects) !== JSON.stringify(incomingProjects);
       const activeChanged = current.activeProjectId !== incomingActive;
 

packages/web/server/lib/opencode/settings-runtime.js

@@ -440,7 +440,13 @@ export const createSettingsRuntime = (deps) => {
   const writeSettingsToDisk = async (settings) => {
     try {
       await fsPromises.mkdir(path.dirname(SETTINGS_FILE_PATH), { recursive: true });
-      await fsPromises.writeFile(SETTINGS_FILE_PATH, JSON.stringify(settings, null, 2), 'utf8');
+      // Atomic write: Electron main and ssh-manager read this file via plain
+      // readFile + JSON.parse and silently coerce parse errors to {}. A
+      // partial read during a non-atomic writeFile would make their next
+      // read-modify-write wipe the settings file.
+      const tmp = `${SETTINGS_FILE_PATH}.tmp-${process.pid}-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
+      await fsPromises.writeFile(tmp, JSON.stringify(settings, null, 2), 'utf8');
+      await fsPromises.rename(tmp, SETTINGS_FILE_PATH);
     } catch (error) {
       console.warn('Failed to write settings file:', error);
       throw error;