fix: resolve data directory persistence between Electron and Web modes

apps/server/src/index.ts

@@ -91,6 +91,9 @@ const PORT = parseInt(process.env.PORT || '3008', 10);
 const HOST = process.env.HOST || '0.0.0.0';
 const HOSTNAME = process.env.HOSTNAME || 'localhost';
 const DATA_DIR = process.env.DATA_DIR || './data';
+logger.info('[SERVER_STARTUP] process.env.DATA_DIR:', process.env.DATA_DIR);
+logger.info('[SERVER_STARTUP] Resolved DATA_DIR:', DATA_DIR);
+logger.info('[SERVER_STARTUP] process.cwd():', process.cwd());
 const ENABLE_REQUEST_LOGGING_DEFAULT = process.env.ENABLE_REQUEST_LOGGING !== 'false'; // Default to true
 
 // Runtime-configurable request logging flag (can be changed via settings)
@@ -175,14 +178,25 @@ app.use(
         return;
       }
 
-      // For local development, allow localhost origins
-      if (
-        origin.startsWith('http://localhost:') ||
-        origin.startsWith('http://127.0.0.1:') ||
-        origin.startsWith('http://[::1]:')
-      ) {
-        callback(null, origin);
-        return;
+      // For local development, allow all localhost/loopback origins (any port)
+      try {
+        const url = new URL(origin);
+        const hostname = url.hostname;
+
+        if (
+          hostname === 'localhost' ||
+          hostname === '127.0.0.1' ||
+          hostname === '::1' ||
+          hostname === '0.0.0.0' ||
+          hostname.startsWith('192.168.') ||
+          hostname.startsWith('10.') ||
+          hostname.startsWith('172.')
+        ) {
+          callback(null, origin);
+          return;
+        }
+      } catch (err) {
+        // Ignore URL parsing errors
       }
 
       // Reject other origins by default for security

apps/server/src/lib/worktree-metadata.ts

@@ -5,18 +5,14 @@
 
 import * as secureFs from './secure-fs.js';
 import * as path from 'path';
+import type { PRState, WorktreePRInfo } from '@automaker/types';
+
+// Re-export types for backwards compatibility
+export type { PRState, WorktreePRInfo };
 
 /** Maximum length for sanitized branch names in filesystem paths */
 const MAX_SANITIZED_BRANCH_PATH_LENGTH = 200;
 
-export interface WorktreePRInfo {
-  number: number;
-  url: string;
-  title: string;
-  state: string;
-  createdAt: string;
-}
-
 export interface WorktreeMetadata {
   branch: string;
   createdAt: string;

apps/server/src/routes/settings/routes/update-global.ts

@@ -45,18 +45,24 @@ export function createUpdateGlobalHandler(settingsService: SettingsService) {
       }
 
       // Minimal debug logging to help diagnose accidental wipes.
-      if ('projects' in updates || 'theme' in updates || 'localStorageMigrated' in updates) {
-        const projectsLen = Array.isArray((updates as any).projects)
-          ? (updates as any).projects.length
-          : undefined;
-        logger.info(
-          `Update global settings request: projects=${projectsLen ?? 'n/a'}, theme=${
-            (updates as any).theme ?? 'n/a'
-          }, localStorageMigrated=${(updates as any).localStorageMigrated ?? 'n/a'}`
-        );
-      }
+      const projectsLen = Array.isArray((updates as any).projects)
+        ? (updates as any).projects.length
+        : undefined;
+      const trashedLen = Array.isArray((updates as any).trashedProjects)
+        ? (updates as any).trashedProjects.length
+        : undefined;
+      logger.info(
+        `[SERVER_SETTINGS_UPDATE] Request received: projects=${projectsLen ?? 'n/a'}, trashedProjects=${trashedLen ?? 'n/a'}, theme=${
+          (updates as any).theme ?? 'n/a'
+        }, localStorageMigrated=${(updates as any).localStorageMigrated ?? 'n/a'}`
+      );
 
+      logger.info('[SERVER_SETTINGS_UPDATE] Calling updateGlobalSettings...');
       const settings = await settingsService.updateGlobalSettings(updates);
+      logger.info(
+        '[SERVER_SETTINGS_UPDATE] Update complete, projects count:',
+        settings.projects?.length ?? 0
+      );
 
       // Apply server log level if it was updated
       if ('serverLogLevel' in updates && updates.serverLogLevel) {

apps/server/src/routes/worktree/routes/create-pr.ts

@@ -13,6 +13,7 @@ import {
 } from '../common.js';
 import { updateWorktreePRInfo } from '../../../lib/worktree-metadata.js';
 import { createLogger } from '@automaker/utils';
+import { validatePRState } from '@automaker/types';
 
 const logger = createLogger('CreatePR');
 
@@ -268,11 +269,12 @@ export function createCreatePRHandler() {
             prAlreadyExisted = true;
 
             // Store the existing PR info in metadata
+            // GitHub CLI returns uppercase states: OPEN, MERGED, CLOSED
             await updateWorktreePRInfo(effectiveProjectPath, branchName, {
               number: existingPr.number,
               url: existingPr.url,
               title: existingPr.title || title,
-              state: existingPr.state || 'open',
+              state: validatePRState(existingPr.state),
               createdAt: new Date().toISOString(),
             });
             logger.debug(
@@ -319,11 +321,12 @@ export function createCreatePRHandler() {
 
               if (prNumber) {
                 try {
+                  // Note: GitHub doesn't have a 'DRAFT' state - drafts still show as 'OPEN'
                   await updateWorktreePRInfo(effectiveProjectPath, branchName, {
                     number: prNumber,
                     url: prUrl,
                     title,
-                    state: draft ? 'draft' : 'open',
+                    state: 'OPEN',
                     createdAt: new Date().toISOString(),
                   });
                   logger.debug(`Stored PR info for branch ${branchName}: PR #${prNumber}`);
@@ -352,11 +355,12 @@ export function createCreatePRHandler() {
                   prNumber = existingPr.number;
                   prAlreadyExisted = true;
 
+                  // GitHub CLI returns uppercase states: OPEN, MERGED, CLOSED
                   await updateWorktreePRInfo(effectiveProjectPath, branchName, {
                     number: existingPr.number,
                     url: existingPr.url,
                     title: existingPr.title || title,
-                    state: existingPr.state || 'open',
+                    state: validatePRState(existingPr.state),
                     createdAt: new Date().toISOString(),
                   });
                   logger.debug(`Fetched and stored existing PR: #${existingPr.number}`);

apps/server/src/routes/worktree/routes/list.ts

@@ -14,8 +14,13 @@ import path from 'path';
 import * as secureFs from '../../../lib/secure-fs.js';
 import { isGitRepo } from '@automaker/git-utils';
 import { getErrorMessage, logError, normalizePath, execEnv, isGhCliAvailable } from '../common.js';
-import { readAllWorktreeMetadata, type WorktreePRInfo } from '../../../lib/worktree-metadata.js';
+import {
+  readAllWorktreeMetadata,
+  updateWorktreePRInfo,
+  type WorktreePRInfo,
+} from '../../../lib/worktree-metadata.js';
 import { createLogger } from '@automaker/utils';
+import { validatePRState } from '@automaker/types';
 import {
   checkGitHubRemote,
   type GitHubRemoteStatus,
@@ -168,8 +173,11 @@ async function getGitHubRemoteStatus(projectPath: string): Promise<GitHubRemoteS
 }
 
 /**
- * Fetch open PRs from GitHub and create a map of branch name to PR info.
- * This allows detecting PRs that were created outside the app.
+ * Fetch all PRs from GitHub and create a map of branch name to PR info.
+ * Uses --state all to include merged/closed PRs, allowing detection of
+ * state changes (e.g., when a PR is merged on GitHub).
+ *
+ * This also allows detecting PRs that were created outside the app.
  *
  * Uses cached GitHub remote status to avoid repeated warnings when the
  * project doesn't have a GitHub remote configured.
@@ -192,9 +200,9 @@ async function fetchGitHubPRs(projectPath: string): Promise<Map<string, Worktree
         ? `-R ${remoteStatus.owner}/${remoteStatus.repo}`
         : '';
 
-    // Fetch open PRs from GitHub
+    // Fetch all PRs from GitHub (including merged/closed to detect state changes)
     const { stdout } = await execAsync(
-      `gh pr list ${repoFlag} --state open --json number,title,url,state,headRefName,createdAt --limit 1000`,
+      `gh pr list ${repoFlag} --state all --json number,title,url,state,headRefName,createdAt --limit 1000`,
       { cwd: projectPath, env: execEnv, timeout: 15000 }
     );
 
@@ -212,7 +220,8 @@ async function fetchGitHubPRs(projectPath: string): Promise<Map<string, Worktree
         number: pr.number,
         url: pr.url,
         title: pr.title,
-        state: pr.state,
+        // GitHub CLI returns state as uppercase: OPEN, MERGED, CLOSED
+        state: validatePRState(pr.state),
         createdAt: pr.createdAt,
       });
     }
@@ -351,23 +360,36 @@ export function createListHandler() {
         }
       }
 
-      // Add PR info from metadata or GitHub for each worktree
-      // Only fetch GitHub PRs if includeDetails is requested (performance optimization)
+      // Assign PR info to each worktree, preferring fresh GitHub data over cached metadata.
+      // Only fetch GitHub PRs if includeDetails is requested (performance optimization).
+      // Uses --state all to detect merged/closed PRs, limited to 1000 recent PRs.
       const githubPRs = includeDetails
         ? await fetchGitHubPRs(projectPath)
         : new Map<string, WorktreePRInfo>();
 
       for (const worktree of worktrees) {
         const metadata = allMetadata.get(worktree.branch);
-        if (metadata?.pr) {
-          // Use stored metadata (more complete info)
-          worktree.pr = metadata.pr;
-        } else if (includeDetails) {
-          // Fall back to GitHub PR detection only when includeDetails is requested
-          const githubPR = githubPRs.get(worktree.branch);
-          if (githubPR) {
-            worktree.pr = githubPR;
+        const githubPR = githubPRs.get(worktree.branch);
+
+        if (githubPR) {
+          // Prefer fresh GitHub data (it has the current state)
+          worktree.pr = githubPR;
+
+          // Sync metadata with GitHub state when:
+          // 1. No metadata exists for this PR (PR created externally)
+          // 2. State has changed (e.g., merged/closed on GitHub)
+          const needsSync = !metadata?.pr || metadata.pr.state !== githubPR.state;
+          if (needsSync) {
+            // Fire and forget - don't block the response
+            updateWorktreePRInfo(projectPath, worktree.branch, githubPR).catch((err) => {
+              logger.warn(
+                `Failed to update PR info for ${worktree.branch}: ${getErrorMessage(err)}`
+              );
+            });
           }
+        } else if (metadata?.pr) {
+          // Fall back to stored metadata (for PRs not in recent GitHub response)
+          worktree.pr = metadata.pr;
         }
       }
 

apps/server/src/services/settings-service.ts

@@ -273,13 +273,39 @@ export class SettingsService {
     };
 
     const currentProjectsLen = Array.isArray(current.projects) ? current.projects.length : 0;
+    // Check if this is a legitimate project removal (moved to trash) vs accidental wipe
+    const newTrashedProjectsLen = Array.isArray(sanitizedUpdates.trashedProjects)
+      ? sanitizedUpdates.trashedProjects.length
+      : Array.isArray(current.trashedProjects)
+        ? current.trashedProjects.length
+        : 0;
+
     if (
       Array.isArray(sanitizedUpdates.projects) &&
       sanitizedUpdates.projects.length === 0 &&
       currentProjectsLen > 0
     ) {
-      attemptedProjectWipe = true;
-      delete sanitizedUpdates.projects;
+      // Only treat as accidental wipe if trashedProjects is also empty
+      // (If projects are moved to trash, they appear in trashedProjects)
+      if (newTrashedProjectsLen === 0) {
+        logger.warn(
+          '[WIPE_PROTECTION] Attempted to set projects to empty array with no trash! Ignoring update.',
+          {
+            currentProjectsLen,
+            newProjectsLen: 0,
+            newTrashedProjectsLen,
+            currentProjects: current.projects?.map((p) => p.name),
+          }
+        );
+        attemptedProjectWipe = true;
+        delete sanitizedUpdates.projects;
+      } else {
+        logger.info('[LEGITIMATE_REMOVAL] Removing all projects to trash', {
+          currentProjectsLen,
+          newProjectsLen: 0,
+          movedToTrash: newTrashedProjectsLen,
+        });
+      }
     }
 
     ignoreEmptyArrayOverwrite('trashedProjects');

apps/server/tests/unit/lib/worktree-metadata.test.ts

@@ -121,7 +121,7 @@ describe('worktree-metadata.ts', () => {
           number: 123,
           url: 'https://github.com/owner/repo/pull/123',
           title: 'Test PR',
-          state: 'open',
+          state: 'OPEN',
           createdAt: new Date().toISOString(),
         },
       };
@@ -158,7 +158,7 @@ describe('worktree-metadata.ts', () => {
           number: 456,
           url: 'https://github.com/owner/repo/pull/456',
           title: 'Updated PR',
-          state: 'closed',
+          state: 'CLOSED',
           createdAt: new Date().toISOString(),
         },
       };
@@ -177,7 +177,7 @@ describe('worktree-metadata.ts', () => {
         number: 789,
         url: 'https://github.com/owner/repo/pull/789',
         title: 'New PR',
-        state: 'open',
+        state: 'OPEN',
         createdAt: new Date().toISOString(),
       };
 
@@ -201,7 +201,7 @@ describe('worktree-metadata.ts', () => {
         number: 999,
         url: 'https://github.com/owner/repo/pull/999',
         title: 'Updated PR',
-        state: 'merged',
+        state: 'MERGED',
         createdAt: new Date().toISOString(),
       };
 
@@ -224,7 +224,7 @@ describe('worktree-metadata.ts', () => {
         number: 111,
         url: 'https://github.com/owner/repo/pull/111',
         title: 'PR',
-        state: 'open',
+        state: 'OPEN',
         createdAt: new Date().toISOString(),
       };
 
@@ -259,7 +259,7 @@ describe('worktree-metadata.ts', () => {
         number: 222,
         url: 'https://github.com/owner/repo/pull/222',
         title: 'Has PR',
-        state: 'open',
+        state: 'OPEN',
         createdAt: new Date().toISOString(),
       };
 
@@ -297,7 +297,7 @@ describe('worktree-metadata.ts', () => {
           number: 333,
           url: 'https://github.com/owner/repo/pull/333',
           title: 'PR 3',
-          state: 'open',
+          state: 'OPEN',
           createdAt: new Date().toISOString(),
         },
       };

apps/ui/src/components/claude-usage-popover.tsx

@@ -2,6 +2,7 @@ import { useState, useEffect, useMemo, useCallback } from 'react';
 import { Popover, PopoverContent, PopoverTrigger } from '@/components/ui/popover';
 import { Button } from '@/components/ui/button';
 import { RefreshCw, AlertTriangle, CheckCircle, XCircle, Clock, ExternalLink } from 'lucide-react';
+import { Spinner } from '@/components/ui/spinner';
 import { cn } from '@/lib/utils';
 import { getElectronAPI } from '@/lib/electron';
 import { useAppStore } from '@/store/app-store';
@@ -279,7 +280,7 @@ export function ClaudeUsagePopover() {
           ) : !claudeUsage ? (
             // Loading state
             <div className="flex flex-col items-center justify-center py-8 space-y-2">
-              <RefreshCw className="w-6 h-6 animate-spin text-muted-foreground/50" />
+              <Spinner size="lg" />
               <p className="text-xs text-muted-foreground">Loading usage data...</p>
             </div>
           ) : (

apps/ui/src/components/codex-usage-popover.tsx

@@ -2,6 +2,7 @@ import { useState, useEffect, useMemo, useCallback } from 'react';
 import { Popover, PopoverContent, PopoverTrigger } from '@/components/ui/popover';
 import { Button } from '@/components/ui/button';
 import { RefreshCw, AlertTriangle, CheckCircle, XCircle, Clock, ExternalLink } from 'lucide-react';
+import { Spinner } from '@/components/ui/spinner';
 import { cn } from '@/lib/utils';
 import { getElectronAPI } from '@/lib/electron';
 import { useAppStore } from '@/store/app-store';
@@ -333,7 +334,7 @@ export function CodexUsagePopover() {
           ) : !codexUsage ? (
             // Loading state
             <div className="flex flex-col items-center justify-center py-8 space-y-2">
-              <RefreshCw className="w-6 h-6 animate-spin text-muted-foreground/50" />
+              <Spinner size="lg" />
               <p className="text-xs text-muted-foreground">Loading usage data...</p>
             </div>
           ) : codexUsage.rateLimits ? (