oAI/Models/SyncModels.swift

@@ -39,6 +39,7 @@ enum SyncError: LocalizedError {
     case repoNotCloned
     case secretsDetected([String])
     case parseError(String)
+    case syncInProgress
 
     var errorDescription: String? {
         switch self {
@@ -56,6 +57,8 @@ enum SyncError: LocalizedError {
             return "Secrets detected in conversations: \(secrets.joined(separator: ", ")). Remove before syncing."
         case .parseError(let message):
             return "Failed to parse conversation: \(message)"
+        case .syncInProgress:
+            return "A sync is already in progress. Try again in a moment."
         }
     }
 }

oAI/Services/GitSyncService.swift

@@ -630,6 +630,20 @@ class GitSyncService {
             return
         }
 
+        // Guard against racing autoSync()/syncNow() on the same working tree — this method and
+        // autoSync() are both fired from independent, uncoordinated Tasks (this one at app launch,
+        // autoSync() debounced off chat activity), so without this a pull here could run while
+        // autoSync() is mid-export, leaving a freshly-written untracked file (folders.json,
+        // notes.json) that the pull then refuses to merge over: "untracked working tree files
+        // would be overwritten by merge." Skipping outright (not waiting) is fine here since
+        // startup sync is a one-time best-effort fetch, not something the user is blocked on.
+        guard !isSyncing else {
+            log.debug("Skipping startup sync (another sync already in progress)")
+            return
+        }
+        isSyncing = true
+        defer { isSyncing = false }
+
         log.info("Running startup sync (pull + import)...")
 
         do {
@@ -668,6 +682,12 @@ class GitSyncService {
 
         // Schedule new sync with 5 second delay
         pendingSyncTask = Task {
+            // Tracks whether *this* task is the one holding isSyncing, so the catch block below
+            // only ever releases a lock it actually acquired — without this, a cancellation while
+            // still waiting in the loop below (i.e. before this task owns the lock at all) would
+            // incorrectly clear isSyncing out from under whichever other sync is still running.
+            var acquiredLock = false
+
             do {
                 // Wait for debounce period
                 try await Task.sleep(for: .seconds(5))
@@ -675,11 +695,23 @@ class GitSyncService {
                 // Check if cancelled during sleep
                 guard !Task.isCancelled else { return }
 
+                // Wait for any other sync (startup pull, manual Sync Now) already in flight to
+                // finish rather than racing it on the same working tree — see syncOnStartup()'s
+                // guard for what goes wrong otherwise. Waiting (not skipping) here, since
+                // auto-sync is how local changes actually reach the remote; silently dropping this
+                // round could leave a push pending indefinitely if nothing else triggers autoSync
+                // again soon.
+                while await MainActor.run(body: { isSyncing }) {
+                    guard !Task.isCancelled else { return }
+                    try await Task.sleep(for: .milliseconds(500))
+                }
+
                 // Set syncing state
                 await MainActor.run {
                     isSyncing = true
                     lastSyncError = nil
                 }
+                acquiredLock = true
 
                 log.info("Auto-sync starting (export + push)...")
 
@@ -694,14 +726,17 @@ class GitSyncService {
                     isSyncing = false
                     syncStatus.lastSyncTime = Date()
                 }
+                acquiredLock = false
 
                 log.info("Auto-sync completed successfully")
 
             } catch {
-                // Error
-                await MainActor.run {
-                    isSyncing = false
-                    lastSyncError = error.localizedDescription
+                // Error — only release the lock if this task actually acquired it
+                if acquiredLock {
+                    await MainActor.run {
+                        isSyncing = false
+                        lastSyncError = error.localizedDescription
+                    }
                 }
 
                 log.error("Auto-sync failed: \(error.localizedDescription)")
@@ -712,6 +747,27 @@ class GitSyncService {
         await pendingSyncTask?.value
     }
 
+    /// Manual full sync (the Settings → Sync "Sync Now" button): pull → import → export → push,
+    /// in that order so the working tree is fully merged before Confab writes its own files back
+    /// out (see exportAllConversations's ordering note). Throws `.syncInProgress` rather than
+    /// racing autoSync()/syncOnStartup() if either is already running on the same working tree —
+    /// same class of bug as the "untracked working tree files" failure those two guard against.
+    func syncNow() async throws -> (imported: Int, skipped: Int) {
+        guard !isSyncing else {
+            throw SyncError.syncInProgress
+        }
+        isSyncing = true
+        defer { isSyncing = false }
+
+        try await pull()
+        let result = try await importAllConversations()
+        try await exportAllConversations()
+        try await push()
+
+        await updateStatus()
+        return (result.imported, result.skipped)
+    }
+
     // MARK: - Secret Scanning
 
     /// Scan for API keys and secrets in conversations

oAI/Views/Screens/SettingsView.swift

@@ -3039,31 +3039,13 @@ It's better to admit "I need more information" or "I cannot do that" than to fak
 
     private func syncNow() async {
         isSyncing = true
-        syncTestResult = nil
+        syncTestResult = "Syncing..."
 
         do {
-            // Step 1: Pull from remote first, into a working tree that hasn't been touched by
-            // this round's export yet. Exporting before pulling can write files (e.g.
-            // folders.json, which every machine writes to the same path) that git then refuses
-            // to merge over: "untracked working tree files would be overwritten by merge".
-            syncTestResult = "Pulling changes..."
-            try await gitSync.pull()
-
-            // Step 2: Import any new/updated conversations and folders from what was just pulled
-            syncTestResult = "Importing conversations..."
-            let result = try await gitSync.importAllConversations()
-
-            // Step 3: Export — now safe, re-derives working tree files from the local DB state,
-            // which already reflects whatever was just imported plus this machine's own changes
-            syncTestResult = "Exporting conversations..."
-            try await gitSync.exportAllConversations()
-
-            // Step 4: Push to remote
-            syncTestResult = "Pushing changes..."
-            try await gitSync.push()
-
-            // Success
-            await gitSync.updateStatus()
+            // Orchestration (pull → import → export → push) and the guard against racing
+            // autoSync()/syncOnStartup() on the same working tree both live in GitSyncService now
+            // — see its syncNow() for why.
+            let result = try await gitSync.syncNow()
             syncTestResult = "✓ Sync complete: \(result.imported) imported, \(result.skipped) skipped"
         } catch {
             syncTestResult = "✗ Sync failed: \(error.localizedDescription)"