completly remove sandbox related code as the downstream libraries do not work with it on various os

apps/ui/src/components/dialogs/index.ts

@@ -3,6 +3,4 @@ export { DeleteAllArchivedSessionsDialog } from './delete-all-archived-sessions-
 export { DeleteSessionDialog } from './delete-session-dialog';
 export { FileBrowserDialog } from './file-browser-dialog';
 export { NewProjectModal } from './new-project-modal';
-export { SandboxRejectionScreen } from './sandbox-rejection-screen';
-export { SandboxRiskDialog } from './sandbox-risk-dialog';
 export { WorkspacePickerModal } from './workspace-picker-modal';

apps/ui/src/components/dialogs/sandbox-rejection-screen.tsx

@@ -1,93 +0,0 @@
-/**
- * Sandbox Rejection Screen
- *
- * Shown in web mode when user denies the sandbox risk confirmation.
- * Prompts them to either restart the app in a container or reload to try again.
- */
-
-import { useState } from 'react';
-import { createLogger } from '@automaker/utils/logger';
-import { ShieldX, RefreshCw, Container, Copy, Check } from 'lucide-react';
-
-const logger = createLogger('SandboxRejectionScreen');
-import { Button } from '@/components/ui/button';
-
-const DOCKER_COMMAND = 'npm run dev:docker';
-
-export function SandboxRejectionScreen() {
-  const [copied, setCopied] = useState(false);
-
-  const handleReload = () => {
-    // Clear the rejection state and reload
-    sessionStorage.removeItem('automaker-sandbox-denied');
-    window.location.reload();
-  };
-
-  const handleCopy = async () => {
-    try {
-      await navigator.clipboard.writeText(DOCKER_COMMAND);
-      setCopied(true);
-      setTimeout(() => setCopied(false), 2000);
-    } catch (err) {
-      logger.error('Failed to copy:', err);
-    }
-  };
-
-  return (
-    <div className="min-h-screen bg-background flex items-center justify-center p-4">
-      <div className="max-w-md w-full text-center space-y-6">
-        <div className="flex justify-center">
-          <div className="rounded-full bg-destructive/10 p-4">
-            <ShieldX className="w-12 h-12 text-destructive" />
-          </div>
-        </div>
-
-        <div className="space-y-2">
-          <h1 className="text-2xl font-semibold">Access Denied</h1>
-          <p className="text-muted-foreground">
-            You declined to accept the risks of running Automaker outside a sandbox environment.
-          </p>
-        </div>
-
-        <div className="bg-muted/50 border border-border rounded-lg p-4 text-left space-y-3">
-          <div className="flex items-start gap-3">
-            <Container className="w-5 h-5 mt-0.5 text-primary flex-shrink-0" />
-            <div className="flex-1 space-y-2">
-              <p className="font-medium text-sm">Run in Docker (Recommended)</p>
-              <p className="text-sm text-muted-foreground">
-                Run Automaker in a containerized sandbox environment:
-              </p>
-              <div className="flex items-center gap-2 bg-background border border-border rounded-lg p-2">
-                <code className="flex-1 text-sm font-mono px-2">{DOCKER_COMMAND}</code>
-                <Button
-                  variant="ghost"
-                  size="sm"
-                  onClick={handleCopy}
-                  className="h-8 px-2 hover:bg-muted"
-                >
-                  {copied ? (
-                    <Check className="w-4 h-4 text-green-500" />
-                  ) : (
-                    <Copy className="w-4 h-4" />
-                  )}
-                </Button>
-              </div>
-            </div>
-          </div>
-        </div>
-
-        <div className="pt-2">
-          <Button
-            variant="outline"
-            onClick={handleReload}
-            className="gap-2"
-            data-testid="sandbox-retry"
-          >
-            <RefreshCw className="w-4 h-4" />
-            Reload &amp; Try Again
-          </Button>
-        </div>
-      </div>
-    </div>
-  );
-}

apps/ui/src/components/dialogs/sandbox-risk-dialog.tsx

@@ -1,140 +0,0 @@
-/**
- * Sandbox Risk Confirmation Dialog
- *
- * Shows when the app is running outside a containerized environment.
- * Users must acknowledge the risks before proceeding.
- */
-
-import { useState } from 'react';
-import { createLogger } from '@automaker/utils/logger';
-import { ShieldAlert, Copy, Check } from 'lucide-react';
-
-const logger = createLogger('SandboxRiskDialog');
-import {
-  Dialog,
-  DialogContent,
-  DialogDescription,
-  DialogFooter,
-  DialogHeader,
-  DialogTitle,
-} from '@/components/ui/dialog';
-import { Button } from '@/components/ui/button';
-import { Checkbox } from '@/components/ui/checkbox';
-import { Label } from '@/components/ui/label';
-
-interface SandboxRiskDialogProps {
-  open: boolean;
-  onConfirm: (skipInFuture: boolean) => void;
-  onDeny: () => void;
-}
-
-const DOCKER_COMMAND = 'npm run dev:docker';
-
-export function SandboxRiskDialog({ open, onConfirm, onDeny }: SandboxRiskDialogProps) {
-  const [copied, setCopied] = useState(false);
-  const [skipInFuture, setSkipInFuture] = useState(false);
-
-  const handleConfirm = () => {
-    onConfirm(skipInFuture);
-    // Reset checkbox state after confirmation
-    setSkipInFuture(false);
-  };
-
-  const handleCopy = async () => {
-    try {
-      await navigator.clipboard.writeText(DOCKER_COMMAND);
-      setCopied(true);
-      setTimeout(() => setCopied(false), 2000);
-    } catch (err) {
-      logger.error('Failed to copy:', err);
-    }
-  };
-
-  return (
-    <Dialog open={open} onOpenChange={() => {}}>
-      <DialogContent
-        className="bg-popover border-border max-w-lg"
-        onPointerDownOutside={(e) => e.preventDefault()}
-        onEscapeKeyDown={(e) => e.preventDefault()}
-        showCloseButton={false}
-      >
-        <DialogHeader>
-          <DialogTitle className="flex items-center gap-2 text-destructive">
-            <ShieldAlert className="w-6 h-6" />
-            Sandbox Environment Not Detected
-          </DialogTitle>
-          <DialogDescription asChild>
-            <div className="space-y-4 pt-2">
-              <p className="text-muted-foreground">
-                <strong>Warning:</strong> This application is running outside of a containerized
-                sandbox environment. AI agents will have direct access to your filesystem and can
-                execute commands on your system.
-              </p>
-
-              <div className="bg-destructive/10 border border-destructive/20 rounded-lg p-4 space-y-2">
-                <p className="text-sm font-medium text-destructive">Potential Risks:</p>
-                <ul className="text-sm text-muted-foreground list-disc list-inside space-y-1">
-                  <li>Agents can read, modify, or delete files on your system</li>
-                  <li>Agents can execute arbitrary commands and install software</li>
-                  <li>Agents can access environment variables and credentials</li>
-                  <li>Unintended side effects from agent actions may affect your system</li>
-                </ul>
-              </div>
-
-              <div className="space-y-2">
-                <p className="text-sm text-muted-foreground">
-                  For safer operation, consider running Automaker in Docker:
-                </p>
-                <div className="flex items-center gap-2 bg-muted/50 border border-border rounded-lg p-2">
-                  <code className="flex-1 text-sm font-mono px-2">{DOCKER_COMMAND}</code>
-                  <Button
-                    variant="ghost"
-                    size="sm"
-                    onClick={handleCopy}
-                    className="h-8 px-2 hover:bg-muted"
-                  >
-                    {copied ? (
-                      <Check className="w-4 h-4 text-green-500" />
-                    ) : (
-                      <Copy className="w-4 h-4" />
-                    )}
-                  </Button>
-                </div>
-              </div>
-            </div>
-          </DialogDescription>
-        </DialogHeader>
-
-        <DialogFooter className="flex-col gap-4 sm:flex-col pt-4">
-          <div className="flex items-center space-x-2 self-start">
-            <Checkbox
-              id="skip-sandbox-warning"
-              checked={skipInFuture}
-              onCheckedChange={(checked) => setSkipInFuture(checked === true)}
-              data-testid="sandbox-skip-checkbox"
-            />
-            <Label
-              htmlFor="skip-sandbox-warning"
-              className="text-sm text-muted-foreground cursor-pointer"
-            >
-              Do not show this warning again
-            </Label>
-          </div>
-          <div className="flex gap-2 sm:gap-2 w-full sm:justify-end">
-            <Button variant="outline" onClick={onDeny} className="px-4" data-testid="sandbox-deny">
-              Deny &amp; Exit
-            </Button>
-            <Button
-              variant="destructive"
-              onClick={handleConfirm}
-              className="px-4"
-              data-testid="sandbox-confirm"
-            >
-              <ShieldAlert className="w-4 h-4 mr-2" />I Accept the Risks
-            </Button>
-          </div>
-        </DialogFooter>
-      </DialogContent>
-    </Dialog>
-  );
-}

apps/ui/src/components/views/board-view.tsx

@@ -89,6 +89,7 @@ export function BoardView() {
     setWorktrees,
     useWorktrees,
     enableDependencyBlocking,
+    skipVerificationInAutoMode,
     isPrimaryWorktreeBranch,
     getPrimaryWorktreeBranch,
     setPipelineConfig,
@@ -732,10 +733,17 @@ export function BoardView() {
   }, []);
 
   useEffect(() => {
+    logger.info(
+      '[AutoMode] Effect triggered - isRunning:',
+      autoMode.isRunning,
+      'hasProject:',
+      !!currentProject
+    );
     if (!autoMode.isRunning || !currentProject) {
       return;
     }
 
+    logger.info('[AutoMode] Starting auto mode polling loop for project:', currentProject.path);
     let isChecking = false;
     let isActive = true; // Track if this effect is still active
 
@@ -755,6 +763,14 @@ export function BoardView() {
       try {
         // Double-check auto mode is still running before proceeding
         if (!isActive || !autoModeRunningRef.current || !currentProject) {
+          logger.debug(
+            '[AutoMode] Skipping check - isActive:',
+            isActive,
+            'autoModeRunning:',
+            autoModeRunningRef.current,
+            'hasProject:',
+            !!currentProject
+          );
           return;
         }
 
@@ -762,6 +778,12 @@ export function BoardView() {
         // Use ref to get the latest running tasks without causing effect re-runs
         const currentRunning = runningAutoTasksRef.current.length + pendingFeaturesRef.current.size;
         const availableSlots = maxConcurrency - currentRunning;
+        logger.debug(
+          '[AutoMode] Checking features - running:',
+          currentRunning,
+          'available slots:',
+          availableSlots
+        );
 
         // No available slots, skip check
         if (availableSlots <= 0) {
@@ -769,10 +791,12 @@ export function BoardView() {
         }
 
         // Filter backlog features by the currently selected worktree branch
-        // This logic mirrors use-board-column-features.ts for consistency
+        // This logic mirrors use-board-column-features.ts for consistency.
+        // HOWEVER: auto mode should still run even if the user is viewing a non-primary worktree,
+        // so we fall back to "all backlog features" when none are visible in the current view.
         // Use ref to get the latest features without causing effect re-runs
         const currentFeatures = hookFeaturesRef.current;
-        const backlogFeatures = currentFeatures.filter((f) => {
+        const backlogFeaturesInView = currentFeatures.filter((f) => {
           if (f.status !== 'backlog') return false;
 
           const featureBranch = f.branchName;
@@ -796,7 +820,25 @@ export function BoardView() {
           return featureBranch === currentWorktreeBranch;
         });
 
+        const backlogFeatures =
+          backlogFeaturesInView.length > 0
+            ? backlogFeaturesInView
+            : currentFeatures.filter((f) => f.status === 'backlog');
+
+        logger.debug(
+          '[AutoMode] Features - total:',
+          currentFeatures.length,
+          'backlog in view:',
+          backlogFeaturesInView.length,
+          'backlog total:',
+          backlogFeatures.length
+        );
+
         if (backlogFeatures.length === 0) {
+          logger.debug(
+            '[AutoMode] No backlog features found, statuses:',
+            currentFeatures.map((f) => f.status).join(', ')
+          );
           return;
         }
 
@@ -806,12 +848,25 @@ export function BoardView() {
         );
 
         // Filter out features with blocking dependencies if dependency blocking is enabled
-        const eligibleFeatures = enableDependencyBlocking
-          ? sortedBacklog.filter((f) => {
-              const blockingDeps = getBlockingDependencies(f, currentFeatures);
-              return blockingDeps.length === 0;
-            })
-          : sortedBacklog;
+        // NOTE: skipVerificationInAutoMode means "ignore unmet dependency verification" so we
+        // should NOT exclude blocked features in that mode.
+        const eligibleFeatures =
+          enableDependencyBlocking && !skipVerificationInAutoMode
+            ? sortedBacklog.filter((f) => {
+                const blockingDeps = getBlockingDependencies(f, currentFeatures);
+                if (blockingDeps.length > 0) {
+                  logger.debug('[AutoMode] Feature', f.id, 'blocked by deps:', blockingDeps);
+                }
+                return blockingDeps.length === 0;
+              })
+            : sortedBacklog;
+
+        logger.debug(
+          '[AutoMode] Eligible features after dep check:',
+          eligibleFeatures.length,
+          'dependency blocking enabled:',
+          enableDependencyBlocking
+        );
 
         // Start features up to available slots
         const featuresToStart = eligibleFeatures.slice(0, availableSlots);
@@ -820,6 +875,13 @@ export function BoardView() {
           return;
         }
 
+        logger.info(
+          '[AutoMode] Starting',
+          featuresToStart.length,
+          'features:',
+          featuresToStart.map((f) => f.id).join(', ')
+        );
+
         for (const feature of featuresToStart) {
           // Check again before starting each feature
           if (!isActive || !autoModeRunningRef.current || !currentProject) {
@@ -827,8 +889,9 @@ export function BoardView() {
           }
 
           // Simplified: No worktree creation on client - server derives workDir from feature.branchName
-          // If feature has no branchName and primary worktree is selected, assign primary branch
-          if (currentWorktreePath === null && !feature.branchName) {
+          // If feature has no branchName, assign it to the primary branch so it can run consistently
+          // even when the user is viewing a non-primary worktree.
+          if (!feature.branchName) {
             const primaryBranch =
               (currentProject.path ? getPrimaryWorktreeBranch(currentProject.path) : null) ||
               'main';
@@ -878,6 +941,7 @@ export function BoardView() {
     getPrimaryWorktreeBranch,
     isPrimaryWorktreeBranch,
     enableDependencyBlocking,
+    skipVerificationInAutoMode,
     persistFeatureUpdate,
   ]);
 

apps/ui/src/components/views/board-view/board-header.tsx

@@ -1,13 +1,15 @@
+import { useState } from 'react';
 import { HotkeyButton } from '@/components/ui/hotkey-button';
 import { Button } from '@/components/ui/button';
 import { Slider } from '@/components/ui/slider';
 import { Switch } from '@/components/ui/switch';
 import { Label } from '@/components/ui/label';
-import { Plus, Bot, Wand2 } from 'lucide-react';
+import { Plus, Bot, Wand2, Settings2 } from 'lucide-react';
 import { KeyboardShortcut } from '@/hooks/use-keyboard-shortcuts';
 import { ClaudeUsagePopover } from '@/components/claude-usage-popover';
 import { useAppStore } from '@/store/app-store';
 import { useSetupStore } from '@/store/setup-store';
+import { AutoModeSettingsDialog } from './dialogs/auto-mode-settings-dialog';
 
 interface BoardHeaderProps {
   projectName: string;
@@ -38,8 +40,11 @@ export function BoardHeader({
   addFeatureShortcut,
   isMounted,
 }: BoardHeaderProps) {
+  const [showAutoModeSettings, setShowAutoModeSettings] = useState(false);
   const apiKeys = useAppStore((state) => state.apiKeys);
   const claudeAuthStatus = useSetupStore((state) => state.claudeAuthStatus);
+  const skipVerificationInAutoMode = useAppStore((state) => state.skipVerificationInAutoMode);
+  const setSkipVerificationInAutoMode = useAppStore((state) => state.setSkipVerificationInAutoMode);
 
   // Hide usage tracking when using API key (only show for Claude Code CLI users)
   // Check both user-entered API key and environment variable ANTHROPIC_API_KEY
@@ -97,9 +102,25 @@ export function BoardHeader({
               onCheckedChange={onAutoModeToggle}
               data-testid="auto-mode-toggle"
             />
+            <button
+              onClick={() => setShowAutoModeSettings(true)}
+              className="p-1 rounded hover:bg-accent/50 transition-colors"
+              title="Auto Mode Settings"
+              data-testid="auto-mode-settings-button"
+            >
+              <Settings2 className="w-4 h-4 text-muted-foreground" />
+            </button>
           </div>
         )}
 
+        {/* Auto Mode Settings Dialog */}
+        <AutoModeSettingsDialog
+          open={showAutoModeSettings}
+          onOpenChange={setShowAutoModeSettings}
+          skipVerificationInAutoMode={skipVerificationInAutoMode}
+          onSkipVerificationChange={setSkipVerificationInAutoMode}
+        />
+
         <Button
           size="sm"
           variant="outline"

apps/ui/src/components/views/board-view/components/kanban-card/card-badges.tsx

@@ -5,118 +5,44 @@ import { Tooltip, TooltipContent, TooltipProvider, TooltipTrigger } from '@/comp
 import { AlertCircle, Lock, Hand, Sparkles } from 'lucide-react';
 import { getBlockingDependencies } from '@automaker/dependency-resolver';
 
-interface CardBadgeProps {
-  children: React.ReactNode;
-  className?: string;
-  'data-testid'?: string;
-  title?: string;
-}
-
-/**
- * Shared badge component matching the "Just Finished" badge style
- * Used for priority badges and other card badges
- */
-function CardBadge({ children, className, 'data-testid': dataTestId, title }: CardBadgeProps) {
-  return (
-    <div
-      className={cn(
-        'inline-flex items-center gap-1 rounded-full border px-1.5 py-0.5 text-[10px] font-medium',
-        className
-      )}
-      data-testid={dataTestId}
-      title={title}
-    >
-      {children}
-    </div>
-  );
-}
+/** Uniform badge style for all card badges */
+const uniformBadgeClass =
+  'inline-flex items-center justify-center w-6 h-6 rounded-md border-[1.5px]';
 
 interface CardBadgesProps {
   feature: Feature;
 }
 
+/**
+ * CardBadges - Shows error badges below the card header
+ * Note: Blocked/Lock badges are now shown in PriorityBadges for visual consistency
+ */
 export function CardBadges({ feature }: CardBadgesProps) {
-  const { enableDependencyBlocking, features } = useAppStore();
-
-  // Calculate blocking dependencies (if feature is in backlog and has incomplete dependencies)
-  const blockingDependencies = useMemo(() => {
-    if (!enableDependencyBlocking || feature.status !== 'backlog') {
-      return [];
-    }
-    return getBlockingDependencies(feature, features);
-  }, [enableDependencyBlocking, feature, features]);
-
-  // Status badges row (error, blocked)
-  const showStatusBadges =
-    feature.error ||
-    (blockingDependencies.length > 0 &&
-      !feature.error &&
-      !feature.skipTests &&
-      feature.status === 'backlog');
-
-  if (!showStatusBadges) {
+  if (!feature.error) {
     return null;
   }
 
   return (
     <div className="flex flex-wrap items-center gap-1.5 px-3 pt-1.5 min-h-[24px]">
       {/* Error badge */}
-      {feature.error && (
-        <TooltipProvider delayDuration={200}>
-          <Tooltip>
-            <TooltipTrigger asChild>
-              <div
-                className={cn(
-                  'inline-flex items-center gap-1 rounded-full border px-1.5 py-0.5 text-[10px] font-medium',
-                  'bg-[var(--status-error-bg)] border-[var(--status-error)]/40 text-[var(--status-error)]'
-                )}
-                data-testid={`error-badge-${feature.id}`}
-              >
-                <AlertCircle className="w-3 h-3" />
-              </div>
-            </TooltipTrigger>
-            <TooltipContent side="bottom" className="text-xs max-w-[250px]">
-              <p>{feature.error}</p>
-            </TooltipContent>
-          </Tooltip>
-        </TooltipProvider>
-      )}
-
-      {/* Blocked badge */}
-      {blockingDependencies.length > 0 &&
-        !feature.error &&
-        !feature.skipTests &&
-        feature.status === 'backlog' && (
-          <TooltipProvider delayDuration={200}>
-            <Tooltip>
-              <TooltipTrigger asChild>
-                <div
-                  className={cn(
-                    'inline-flex items-center gap-1 rounded-full border-2 px-1.5 py-0.5 text-[10px] font-bold',
-                    'bg-orange-500/20 border-orange-500/50 text-orange-500'
-                  )}
-                  data-testid={`blocked-badge-${feature.id}`}
-                >
-                  <Lock className="w-3 h-3" />
-                </div>
-              </TooltipTrigger>
-              <TooltipContent side="bottom" className="text-xs max-w-[250px]">
-                <p className="font-medium mb-1">
-                  Blocked by {blockingDependencies.length} incomplete{' '}
-                  {blockingDependencies.length === 1 ? 'dependency' : 'dependencies'}
-                </p>
-                <p className="text-muted-foreground">
-                  {blockingDependencies
-                    .map((depId) => {
-                      const dep = features.find((f) => f.id === depId);
-                      return dep?.description || depId;
-                    })
-                    .join(', ')}
-                </p>
-              </TooltipContent>
-            </Tooltip>
-          </TooltipProvider>
-        )}
+      <TooltipProvider delayDuration={200}>
+        <Tooltip>
+          <TooltipTrigger asChild>
+            <div
+              className={cn(
+                uniformBadgeClass,
+                'bg-[var(--status-error-bg)] border-[var(--status-error)]/40 text-[var(--status-error)]'
+              )}
+              data-testid={`error-badge-${feature.id}`}
+            >
+              <AlertCircle className="w-3.5 h-3.5" />
+            </div>
+          </TooltipTrigger>
+          <TooltipContent side="bottom" className="text-xs max-w-[250px]">
+            <p>{feature.error}</p>
+          </TooltipContent>
+        </Tooltip>
+      </TooltipProvider>
     </div>
   );
 }
@@ -126,8 +52,17 @@ interface PriorityBadgesProps {
 }
 
 export function PriorityBadges({ feature }: PriorityBadgesProps) {
+  const { enableDependencyBlocking, features } = useAppStore();
   const [currentTime, setCurrentTime] = useState(() => Date.now());
 
+  // Calculate blocking dependencies (if feature is in backlog and has incomplete dependencies)
+  const blockingDependencies = useMemo(() => {
+    if (!enableDependencyBlocking || feature.status !== 'backlog') {
+      return [];
+    }
+    return getBlockingDependencies(feature, features);
+  }, [enableDependencyBlocking, feature, features]);
+
   const isJustFinished = useMemo(() => {
     if (!feature.justFinishedAt || feature.status !== 'waiting_approval' || feature.error) {
       return false;
@@ -161,25 +96,27 @@ export function PriorityBadges({ feature }: PriorityBadgesProps) {
     };
   }, [feature.justFinishedAt, feature.status, currentTime]);
 
-  const showPriorityBadges =
-    feature.priority ||
-    (feature.skipTests && !feature.error && feature.status === 'backlog') ||
-    isJustFinished;
+  const isBlocked =
+    blockingDependencies.length > 0 && !feature.error && feature.status === 'backlog';
+  const showManualVerification =
+    feature.skipTests && !feature.error && feature.status === 'backlog';
 
-  if (!showPriorityBadges) {
+  const showBadges = feature.priority || showManualVerification || isBlocked || isJustFinished;
+
+  if (!showBadges) {
     return null;
   }
 
   return (
-    <div className="absolute top-2 left-2 flex items-center gap-1.5">
+    <div className="absolute top-2 left-2 flex items-center gap-1">
       {/* Priority badge */}
       {feature.priority && (
         <TooltipProvider delayDuration={200}>
           <Tooltip>
             <TooltipTrigger asChild>
-              <CardBadge
+              <div
                 className={cn(
-                  'bg-opacity-90 border rounded-[6px] px-1.5 py-0.5 flex items-center justify-center border-[1.5px] w-5 h-5', // badge style from example
+                  uniformBadgeClass,
                   feature.priority === 1 &&
                     'bg-[var(--status-error-bg)] border-[var(--status-error)]/40 text-[var(--status-error)]',
                   feature.priority === 2 &&
@@ -189,14 +126,10 @@ export function PriorityBadges({ feature }: PriorityBadgesProps) {
                 )}
                 data-testid={`priority-badge-${feature.id}`}
               >
-                {feature.priority === 1 ? (
-                  <span className="font-bold text-xs flex items-center gap-0.5">H</span>
-                ) : feature.priority === 2 ? (
-                  <span className="font-bold text-xs flex items-center gap-0.5">M</span>
-                ) : (
-                  <span className="font-bold text-xs flex items-center gap-0.5">L</span>
-                )}
-              </CardBadge>
+                <span className="font-bold text-xs">
+                  {feature.priority === 1 ? 'H' : feature.priority === 2 ? 'M' : 'L'}
+                </span>
+              </div>
             </TooltipTrigger>
             <TooltipContent side="bottom" className="text-xs">
               <p>
@@ -210,17 +143,21 @@ export function PriorityBadges({ feature }: PriorityBadgesProps) {
           </Tooltip>
         </TooltipProvider>
       )}
+
       {/* Manual verification badge */}
-      {feature.skipTests && !feature.error && feature.status === 'backlog' && (
+      {showManualVerification && (
         <TooltipProvider delayDuration={200}>
           <Tooltip>
             <TooltipTrigger asChild>
-              <CardBadge
-                className="bg-[var(--status-warning-bg)] border-[var(--status-warning)]/40 text-[var(--status-warning)]"
+              <div
+                className={cn(
+                  uniformBadgeClass,
+                  'bg-[var(--status-warning-bg)] border-[var(--status-warning)]/40 text-[var(--status-warning)]'
+                )}
                 data-testid={`skip-tests-badge-${feature.id}`}
               >
-                <Hand className="w-3 h-3" />
-              </CardBadge>
+                <Hand className="w-3.5 h-3.5" />
+              </div>
             </TooltipTrigger>
             <TooltipContent side="bottom" className="text-xs">
               <p>Manual verification required</p>
@@ -229,15 +166,59 @@ export function PriorityBadges({ feature }: PriorityBadgesProps) {
         </TooltipProvider>
       )}
 
+      {/* Blocked badge */}
+      {isBlocked && (
+        <TooltipProvider delayDuration={200}>
+          <Tooltip>
+            <TooltipTrigger asChild>
+              <div
+                className={cn(
+                  uniformBadgeClass,
+                  'bg-orange-500/20 border-orange-500/50 text-orange-500'
+                )}
+                data-testid={`blocked-badge-${feature.id}`}
+              >
+                <Lock className="w-3.5 h-3.5" />
+              </div>
+            </TooltipTrigger>
+            <TooltipContent side="bottom" className="text-xs max-w-[250px]">
+              <p className="font-medium mb-1">
+                Blocked by {blockingDependencies.length} incomplete{' '}
+                {blockingDependencies.length === 1 ? 'dependency' : 'dependencies'}
+              </p>
+              <p className="text-muted-foreground">
+                {blockingDependencies
+                  .map((depId) => {
+                    const dep = features.find((f) => f.id === depId);
+                    return dep?.description || depId;
+                  })
+                  .join(', ')}
+              </p>
+            </TooltipContent>
+          </Tooltip>
+        </TooltipProvider>
+      )}
+
       {/* Just Finished badge */}
       {isJustFinished && (
-        <CardBadge
-          className="bg-[var(--status-success-bg)] border-[var(--status-success)]/40 text-[var(--status-success)] animate-pulse"
-          data-testid={`just-finished-badge-${feature.id}`}
-          title="Agent just finished working on this feature"
-        >
-          <Sparkles className="w-3 h-3" />
-        </CardBadge>
+        <TooltipProvider delayDuration={200}>
+          <Tooltip>
+            <TooltipTrigger asChild>
+              <div
+                className={cn(
+                  uniformBadgeClass,
+                  'bg-[var(--status-success-bg)] border-[var(--status-success)]/40 text-[var(--status-success)] animate-pulse'
+                )}
+                data-testid={`just-finished-badge-${feature.id}`}
+              >
+                <Sparkles className="w-3.5 h-3.5" />
+              </div>
+            </TooltipTrigger>
+            <TooltipContent side="bottom" className="text-xs">
+              <p>Agent just finished working on this feature</p>
+            </TooltipContent>
+          </Tooltip>
+        </TooltipProvider>
       )}
     </div>
   );

apps/ui/src/components/views/board-view/dialogs/auto-mode-settings-dialog.tsx

@@ -0,0 +1,68 @@
+import {
+  Dialog,
+  DialogContent,
+  DialogDescription,
+  DialogHeader,
+  DialogTitle,
+} from '@/components/ui/dialog';
+import { Label } from '@/components/ui/label';
+import { Switch } from '@/components/ui/switch';
+import { FastForward, Settings2 } from 'lucide-react';
+
+interface AutoModeSettingsDialogProps {
+  open: boolean;
+  onOpenChange: (open: boolean) => void;
+  skipVerificationInAutoMode: boolean;
+  onSkipVerificationChange: (value: boolean) => void;
+}
+
+export function AutoModeSettingsDialog({
+  open,
+  onOpenChange,
+  skipVerificationInAutoMode,
+  onSkipVerificationChange,
+}: AutoModeSettingsDialogProps) {
+  return (
+    <Dialog open={open} onOpenChange={onOpenChange}>
+      <DialogContent className="sm:max-w-md" data-testid="auto-mode-settings-dialog">
+        <DialogHeader>
+          <DialogTitle className="flex items-center gap-2">
+            <Settings2 className="w-5 h-5" />
+            Auto Mode Settings
+          </DialogTitle>
+          <DialogDescription>
+            Configure how auto mode handles feature execution and dependencies.
+          </DialogDescription>
+        </DialogHeader>
+
+        <div className="space-y-4 py-4">
+          {/* Skip Verification Setting */}
+          <div className="flex items-start space-x-3 p-3 rounded-lg bg-secondary/50">
+            <div className="flex-1 space-y-1">
+              <div className="flex items-center justify-between">
+                <Label
+                  htmlFor="skip-verification-toggle"
+                  className="text-sm font-medium cursor-pointer flex items-center gap-2"
+                >
+                  <FastForward className="w-4 h-4 text-brand-500" />
+                  Skip verification requirement
+                </Label>
+                <Switch
+                  id="skip-verification-toggle"
+                  checked={skipVerificationInAutoMode}
+                  onCheckedChange={onSkipVerificationChange}
+                  data-testid="skip-verification-toggle"
+                />
+              </div>
+              <p className="text-xs text-muted-foreground leading-relaxed">
+                When enabled, auto mode will grab features even if their dependencies are not
+                verified, as long as they are not currently running. This allows faster pipeline
+                execution without waiting for manual verification.
+              </p>
+            </div>
+          </div>
+        </div>
+      </DialogContent>
+    </Dialog>
+  );
+}

apps/ui/src/components/views/board-view/hooks/use-board-actions.ts

@@ -79,6 +79,7 @@ export function useBoardActions({
     moveFeature,
     useWorktrees,
     enableDependencyBlocking,
+    skipVerificationInAutoMode,
     isPrimaryWorktreeBranch,
     getPrimaryWorktreeBranch,
   } = useAppStore();
@@ -805,12 +806,14 @@ export function useBoardActions({
     // Sort by priority (lower number = higher priority, priority 1 is highest)
     // Features with blocking dependencies are sorted to the end
     const sortedBacklog = [...backlogFeatures].sort((a, b) => {
-      const aBlocked = enableDependencyBlocking
-        ? getBlockingDependencies(a, features).length > 0
-        : false;
-      const bBlocked = enableDependencyBlocking
-        ? getBlockingDependencies(b, features).length > 0
-        : false;
+      const aBlocked =
+        enableDependencyBlocking && !skipVerificationInAutoMode
+          ? getBlockingDependencies(a, features).length > 0
+          : false;
+      const bBlocked =
+        enableDependencyBlocking && !skipVerificationInAutoMode
+          ? getBlockingDependencies(b, features).length > 0
+          : false;
 
       // Blocked features go to the end
       if (aBlocked && !bBlocked) return 1;
@@ -822,14 +825,14 @@ export function useBoardActions({
 
     // Find the first feature without blocking dependencies
     const featureToStart = sortedBacklog.find((f) => {
-      if (!enableDependencyBlocking) return true;
+      if (!enableDependencyBlocking || skipVerificationInAutoMode) return true;
       return getBlockingDependencies(f, features).length === 0;
     });
 
     if (!featureToStart) {
       toast.info('No eligible features', {
         description:
-          'All backlog features have unmet dependencies. Complete their dependencies first.',
+          'All backlog features have unmet dependencies. Complete their dependencies first (or enable "Skip verification requirement" in Auto Mode settings).',
       });
       return;
     }
@@ -846,6 +849,7 @@ export function useBoardActions({
     isPrimaryWorktreeBranch,
     getPrimaryWorktreeBranch,
     enableDependencyBlocking,
+    skipVerificationInAutoMode,
   ]);
 
   const handleArchiveAllVerified = useCallback(async () => {

apps/ui/src/components/views/settings-view.tsx

@@ -31,6 +31,8 @@ export function SettingsView() {
     setDefaultSkipTests,
     enableDependencyBlocking,
     setEnableDependencyBlocking,
+    skipVerificationInAutoMode,
+    setSkipVerificationInAutoMode,
     useWorktrees,
     setUseWorktrees,
     showProfilesOnly,
@@ -48,10 +50,6 @@ export function SettingsView() {
     aiProfiles,
     autoLoadClaudeMd,
     setAutoLoadClaudeMd,
-    enableSandboxMode,
-    setEnableSandboxMode,
-    skipSandboxWarning,
-    setSkipSandboxWarning,
     promptCustomization,
     setPromptCustomization,
   } = useAppStore();
@@ -130,6 +128,7 @@ export function SettingsView() {
             showProfilesOnly={showProfilesOnly}
             defaultSkipTests={defaultSkipTests}
             enableDependencyBlocking={enableDependencyBlocking}
+            skipVerificationInAutoMode={skipVerificationInAutoMode}
             useWorktrees={useWorktrees}
             defaultPlanningMode={defaultPlanningMode}
             defaultRequirePlanApproval={defaultRequirePlanApproval}
@@ -138,6 +137,7 @@ export function SettingsView() {
             onShowProfilesOnlyChange={setShowProfilesOnly}
             onDefaultSkipTestsChange={setDefaultSkipTests}
             onEnableDependencyBlockingChange={setEnableDependencyBlocking}
+            onSkipVerificationInAutoModeChange={setSkipVerificationInAutoMode}
             onUseWorktreesChange={setUseWorktrees}
             onDefaultPlanningModeChange={setDefaultPlanningMode}
             onDefaultRequirePlanApprovalChange={setDefaultRequirePlanApproval}
@@ -149,8 +149,6 @@ export function SettingsView() {
           <DangerZoneSection
             project={settingsProject}
             onDeleteClick={() => setShowDeleteDialog(true)}
-            skipSandboxWarning={skipSandboxWarning}
-            onResetSandboxWarning={() => setSkipSandboxWarning(false)}
           />
         );
       default:

apps/ui/src/components/views/settings-view/claude/claude-md-settings.tsx

@@ -1,13 +1,11 @@
 import { Label } from '@/components/ui/label';
 import { Checkbox } from '@/components/ui/checkbox';
-import { FileCode, Shield } from 'lucide-react';
+import { FileCode } from 'lucide-react';
 import { cn } from '@/lib/utils';
 
 interface ClaudeMdSettingsProps {
   autoLoadClaudeMd: boolean;
   onAutoLoadClaudeMdChange: (enabled: boolean) => void;
-  enableSandboxMode: boolean;
-  onEnableSandboxModeChange: (enabled: boolean) => void;
 }
 
 /**
@@ -15,23 +13,18 @@ interface ClaudeMdSettingsProps {
  *
  * UI controls for Claude Agent SDK settings including:
  * - Auto-loading of project instructions from .claude/CLAUDE.md files
- * - Sandbox mode for isolated bash command execution
  *
  * Usage:
  * ```tsx
  * <ClaudeMdSettings
  *   autoLoadClaudeMd={autoLoadClaudeMd}
  *   onAutoLoadClaudeMdChange={setAutoLoadClaudeMd}
- *   enableSandboxMode={enableSandboxMode}
- *   onEnableSandboxModeChange={setEnableSandboxMode}
  * />
  * ```
  */
 export function ClaudeMdSettings({
   autoLoadClaudeMd,
   onAutoLoadClaudeMdChange,
-  enableSandboxMode,
-  onEnableSandboxModeChange,
 }: ClaudeMdSettingsProps) {
   return (
     <div
@@ -83,32 +76,6 @@ export function ClaudeMdSettings({
             </p>
           </div>
         </div>
-
-        <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3 mt-2">
-          <Checkbox
-            id="enable-sandbox-mode"
-            checked={enableSandboxMode}
-            onCheckedChange={(checked) => onEnableSandboxModeChange(checked === true)}
-            className="mt-1"
-            data-testid="enable-sandbox-mode-checkbox"
-          />
-          <div className="space-y-1.5">
-            <Label
-              htmlFor="enable-sandbox-mode"
-              className="text-foreground cursor-pointer font-medium flex items-center gap-2"
-            >
-              <Shield className="w-4 h-4 text-brand-500" />
-              Enable Sandbox Mode
-            </Label>
-            <p className="text-xs text-muted-foreground/80 leading-relaxed">
-              Run bash commands in an isolated sandbox environment for additional security.
-              <span className="block mt-1 text-warning/80">
-                Note: On some systems, enabling sandbox mode may cause the agent to hang without
-                responding. If you experience issues, try disabling this option.
-              </span>
-            </p>
-          </div>
-        </div>
       </div>
     </div>
   );

apps/ui/src/components/views/settings-view/danger-zone/danger-zone-section.tsx

@@ -1,21 +1,14 @@
 import { Button } from '@/components/ui/button';
-import { Trash2, Folder, AlertTriangle, Shield, RotateCcw } from 'lucide-react';
+import { Trash2, Folder, AlertTriangle } from 'lucide-react';
 import { cn } from '@/lib/utils';
 import type { Project } from '../shared/types';
 
 interface DangerZoneSectionProps {
   project: Project | null;
   onDeleteClick: () => void;
-  skipSandboxWarning: boolean;
-  onResetSandboxWarning: () => void;
 }
 
-export function DangerZoneSection({
-  project,
-  onDeleteClick,
-  skipSandboxWarning,
-  onResetSandboxWarning,
-}: DangerZoneSectionProps) {
+export function DangerZoneSection({ project, onDeleteClick }: DangerZoneSectionProps) {
   return (
     <div
       className={cn(
@@ -37,36 +30,6 @@ export function DangerZoneSection({
         </p>
       </div>
       <div className="p-6 space-y-4">
-        {/* Sandbox Warning Reset */}
-        {skipSandboxWarning && (
-          <div className="flex items-center justify-between gap-4 p-4 rounded-xl bg-destructive/5 border border-destructive/10">
-            <div className="flex items-center gap-3.5 min-w-0">
-              <div className="w-11 h-11 rounded-xl bg-gradient-to-br from-destructive/15 to-destructive/10 border border-destructive/20 flex items-center justify-center shrink-0">
-                <Shield className="w-5 h-5 text-destructive" />
-              </div>
-              <div className="min-w-0">
-                <p className="font-medium text-foreground">Sandbox Warning Disabled</p>
-                <p className="text-xs text-muted-foreground/70 mt-0.5">
-                  The sandbox environment warning is hidden on startup
-                </p>
-              </div>
-            </div>
-            <Button
-              variant="outline"
-              onClick={onResetSandboxWarning}
-              data-testid="reset-sandbox-warning-button"
-              className={cn(
-                'shrink-0 gap-2',
-                'transition-all duration-200 ease-out',
-                'hover:scale-[1.02] active:scale-[0.98]'
-              )}
-            >
-              <RotateCcw className="w-4 h-4" />
-              Reset
-            </Button>
-          </div>
-        )}
-
         {/* Project Delete */}
         {project && (
           <div className="flex items-center justify-between gap-4 p-4 rounded-xl bg-destructive/5 border border-destructive/10">
@@ -97,7 +60,7 @@ export function DangerZoneSection({
         )}
 
         {/* Empty state when nothing to show */}
-        {!skipSandboxWarning && !project && (
+        {!project && (
           <p className="text-sm text-muted-foreground/60 text-center py-4">
             No danger zone actions available.
           </p>

apps/ui/src/components/views/settings-view/feature-defaults/feature-defaults-section.tsx

@@ -12,6 +12,7 @@ import {
   ScrollText,
   ShieldCheck,
   User,
+  FastForward,
 } from 'lucide-react';
 import { cn } from '@/lib/utils';
 import {
@@ -29,6 +30,7 @@ interface FeatureDefaultsSectionProps {
   showProfilesOnly: boolean;
   defaultSkipTests: boolean;
   enableDependencyBlocking: boolean;
+  skipVerificationInAutoMode: boolean;
   useWorktrees: boolean;
   defaultPlanningMode: PlanningMode;
   defaultRequirePlanApproval: boolean;
@@ -37,6 +39,7 @@ interface FeatureDefaultsSectionProps {
   onShowProfilesOnlyChange: (value: boolean) => void;
   onDefaultSkipTestsChange: (value: boolean) => void;
   onEnableDependencyBlockingChange: (value: boolean) => void;
+  onSkipVerificationInAutoModeChange: (value: boolean) => void;
   onUseWorktreesChange: (value: boolean) => void;
   onDefaultPlanningModeChange: (value: PlanningMode) => void;
   onDefaultRequirePlanApprovalChange: (value: boolean) => void;
@@ -47,6 +50,7 @@ export function FeatureDefaultsSection({
   showProfilesOnly,
   defaultSkipTests,
   enableDependencyBlocking,
+  skipVerificationInAutoMode,
   useWorktrees,
   defaultPlanningMode,
   defaultRequirePlanApproval,
@@ -55,6 +59,7 @@ export function FeatureDefaultsSection({
   onShowProfilesOnlyChange,
   onDefaultSkipTestsChange,
   onEnableDependencyBlockingChange,
+  onSkipVerificationInAutoModeChange,
   onUseWorktreesChange,
   onDefaultPlanningModeChange,
   onDefaultRequirePlanApprovalChange,
@@ -309,6 +314,34 @@ export function FeatureDefaultsSection({
         {/* Separator */}
         <div className="border-t border-border/30" />
 
+        {/* Skip Verification in Auto Mode Setting */}
+        <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3">
+          <Checkbox
+            id="skip-verification-auto-mode"
+            checked={skipVerificationInAutoMode}
+            onCheckedChange={(checked) => onSkipVerificationInAutoModeChange(checked === true)}
+            className="mt-1"
+            data-testid="skip-verification-auto-mode-checkbox"
+          />
+          <div className="space-y-1.5">
+            <Label
+              htmlFor="skip-verification-auto-mode"
+              className="text-foreground cursor-pointer font-medium flex items-center gap-2"
+            >
+              <FastForward className="w-4 h-4 text-brand-500" />
+              Skip verification in auto mode
+            </Label>
+            <p className="text-xs text-muted-foreground/80 leading-relaxed">
+              When enabled, auto mode will grab features even if their dependencies are not
+              verified, as long as they are not currently running. This allows faster pipeline
+              execution without waiting for manual verification.
+            </p>
+          </div>
+        </div>
+
+        {/* Separator */}
+        <div className="border-t border-border/30" />
+
         {/* Worktree Isolation Setting */}
         <div className="group flex items-start space-x-3 p-3 rounded-xl hover:bg-accent/30 transition-colors duration-200 -mx-3">
           <Checkbox

apps/ui/src/hooks/use-auto-mode.ts

@@ -7,6 +7,36 @@ import type { AutoModeEvent } from '@/types/electron';
 
 const logger = createLogger('AutoMode');
 
+const AUTO_MODE_SESSION_KEY = 'automaker:autoModeRunningByProjectPath';
+
+function readAutoModeSession(): Record<string, boolean> {
+  try {
+    if (typeof window === 'undefined') return {};
+    const raw = window.sessionStorage?.getItem(AUTO_MODE_SESSION_KEY);
+    if (!raw) return {};
+    const parsed = JSON.parse(raw) as unknown;
+    if (!parsed || typeof parsed !== 'object') return {};
+    return parsed as Record<string, boolean>;
+  } catch {
+    return {};
+  }
+}
+
+function writeAutoModeSession(next: Record<string, boolean>): void {
+  try {
+    if (typeof window === 'undefined') return;
+    window.sessionStorage?.setItem(AUTO_MODE_SESSION_KEY, JSON.stringify(next));
+  } catch {
+    // ignore storage errors (private mode, disabled storage, etc.)
+  }
+}
+
+function setAutoModeSessionForProjectPath(projectPath: string, running: boolean): void {
+  const current = readAutoModeSession();
+  const next = { ...current, [projectPath]: running };
+  writeAutoModeSession(next);
+}
+
 // Type guard for plan_approval_required event
 function isPlanApprovalEvent(
   event: AutoModeEvent
@@ -64,6 +94,23 @@ export function useAutoMode() {
   // Check if we can start a new task based on concurrency limit
   const canStartNewTask = runningAutoTasks.length < maxConcurrency;
 
+  // Restore auto-mode toggle after a renderer refresh (e.g. dev HMR reload).
+  // This is intentionally session-scoped to avoid auto-running features after a full app restart.
+  useEffect(() => {
+    if (!currentProject) return;
+
+    const session = readAutoModeSession();
+    const desired = session[currentProject.path];
+    if (typeof desired !== 'boolean') return;
+
+    if (desired !== isAutoModeRunning) {
+      logger.info(
+        `[AutoMode] Restoring session state for ${currentProject.path}: ${desired ? 'ON' : 'OFF'}`
+      );
+      setAutoModeRunning(currentProject.id, desired);
+    }
+  }, [currentProject, isAutoModeRunning, setAutoModeRunning]);
+
   // Handle auto mode events - listen globally for all projects
   useEffect(() => {
     const api = getElectronAPI();
@@ -337,6 +384,7 @@ export function useAutoMode() {
       return;
     }
 
+    setAutoModeSessionForProjectPath(currentProject.path, true);
     setAutoModeRunning(currentProject.id, true);
     logger.debug(`[AutoMode] Started with maxConcurrency: ${maxConcurrency}`);
   }, [currentProject, setAutoModeRunning, maxConcurrency]);
@@ -348,6 +396,7 @@ export function useAutoMode() {
       return;
     }
 
+    setAutoModeSessionForProjectPath(currentProject.path, false);
     setAutoModeRunning(currentProject.id, false);
     // NOTE: We intentionally do NOT clear running tasks here.
     // Stopping auto mode only turns off the toggle to prevent new features

apps/ui/src/hooks/use-settings-migration.ts

@@ -23,6 +23,7 @@ import { getHttpApiClient, waitForApiKeyInit } from '@/lib/http-api-client';
 import { isElectron } from '@/lib/electron';
 import { getItem, removeItem } from '@/lib/storage';
 import { useAppStore } from '@/store/app-store';
+import type { GlobalSettings } from '@automaker/types';
 
 const logger = createLogger('SettingsMigration');
 
@@ -123,7 +124,63 @@ export function useSettingsMigration(): MigrationState {
 
         // If settings files already exist, no migration needed
         if (!status.needsMigration) {
-          logger.info('Settings files exist, no migration needed');
+          logger.info('Settings files exist - hydrating UI store from server');
+
+          // IMPORTANT: the server settings file is now the source of truth.
+          // If localStorage/Zustand get out of sync (e.g. cleared localStorage),
+          // the UI can show stale values even though the server will execute with
+          // the file-based settings. Hydrate the store from the server on startup.
+          try {
+            const global = await api.settings.getGlobal();
+            if (global.success && global.settings) {
+              const serverSettings = global.settings as unknown as GlobalSettings;
+              const current = useAppStore.getState();
+
+              useAppStore.setState({
+                theme: serverSettings.theme as unknown as import('@/store/app-store').ThemeMode,
+                sidebarOpen: serverSettings.sidebarOpen,
+                chatHistoryOpen: serverSettings.chatHistoryOpen,
+                kanbanCardDetailLevel: serverSettings.kanbanCardDetailLevel,
+                maxConcurrency: serverSettings.maxConcurrency,
+                defaultSkipTests: serverSettings.defaultSkipTests,
+                enableDependencyBlocking: serverSettings.enableDependencyBlocking,
+                skipVerificationInAutoMode: serverSettings.skipVerificationInAutoMode,
+                useWorktrees: serverSettings.useWorktrees,
+                showProfilesOnly: serverSettings.showProfilesOnly,
+                defaultPlanningMode: serverSettings.defaultPlanningMode,
+                defaultRequirePlanApproval: serverSettings.defaultRequirePlanApproval,
+                defaultAIProfileId: serverSettings.defaultAIProfileId,
+                muteDoneSound: serverSettings.muteDoneSound,
+                enhancementModel: serverSettings.enhancementModel,
+                validationModel: serverSettings.validationModel,
+                phaseModels: serverSettings.phaseModels,
+                enabledCursorModels: serverSettings.enabledCursorModels,
+                cursorDefaultModel: serverSettings.cursorDefaultModel,
+                autoLoadClaudeMd: serverSettings.autoLoadClaudeMd ?? false,
+                keyboardShortcuts: {
+                  ...current.keyboardShortcuts,
+                  ...(serverSettings.keyboardShortcuts as unknown as Partial<
+                    typeof current.keyboardShortcuts
+                  >),
+                },
+                aiProfiles: serverSettings.aiProfiles,
+                mcpServers: serverSettings.mcpServers,
+                promptCustomization: serverSettings.promptCustomization ?? {},
+                projects: serverSettings.projects,
+                trashedProjects: serverSettings.trashedProjects,
+                projectHistory: serverSettings.projectHistory,
+                projectHistoryIndex: serverSettings.projectHistoryIndex,
+                lastSelectedSessionByProject: serverSettings.lastSelectedSessionByProject,
+              });
+
+              logger.info('Hydrated UI settings from server settings file');
+            } else {
+              logger.warn('Failed to load global settings from server:', global);
+            }
+          } catch (error) {
+            logger.error('Failed to hydrate UI settings from server:', error);
+          }
+
           setState({ checked: true, migrated: false, error: null });
           return;
         }
@@ -201,14 +258,28 @@ export function useSettingsMigration(): MigrationState {
 export async function syncSettingsToServer(): Promise<boolean> {
   try {
     const api = getHttpApiClient();
-    const automakerStorage = getItem('automaker-storage');
-
-    if (!automakerStorage) {
-      return false;
+    // IMPORTANT:
+    // Prefer the live Zustand state over localStorage to avoid race conditions
+    // (Zustand persistence writes can lag behind `set(...)`, which would cause us
+    // to sync stale values to the server).
+    //
+    // localStorage remains as a fallback for cases where the store isn't ready.
+    let state: Record<string, unknown> | null = null;
+    try {
+      state = useAppStore.getState() as unknown as Record<string, unknown>;
+    } catch {
+      // Ignore and fall back to localStorage
     }
 
-    const parsed = JSON.parse(automakerStorage);
-    const state = parsed.state || parsed;
+    if (!state) {
+      const automakerStorage = getItem('automaker-storage');
+      if (!automakerStorage) {
+        return false;
+      }
+
+      const parsed = JSON.parse(automakerStorage) as Record<string, unknown>;
+      state = (parsed.state as Record<string, unknown> | undefined) || parsed;
+    }
 
     // Extract settings to sync
     const updates = {
@@ -219,6 +290,7 @@ export async function syncSettingsToServer(): Promise<boolean> {
       maxConcurrency: state.maxConcurrency,
       defaultSkipTests: state.defaultSkipTests,
       enableDependencyBlocking: state.enableDependencyBlocking,
+      skipVerificationInAutoMode: state.skipVerificationInAutoMode,
       useWorktrees: state.useWorktrees,
       showProfilesOnly: state.showProfilesOnly,
       defaultPlanningMode: state.defaultPlanningMode,
@@ -229,8 +301,6 @@ export async function syncSettingsToServer(): Promise<boolean> {
       validationModel: state.validationModel,
       phaseModels: state.phaseModels,
       autoLoadClaudeMd: state.autoLoadClaudeMd,
-      enableSandboxMode: state.enableSandboxMode,
-      skipSandboxWarning: state.skipSandboxWarning,
       keyboardShortcuts: state.keyboardShortcuts,
       aiProfiles: state.aiProfiles,
       mcpServers: state.mcpServers,

apps/ui/src/lib/http-api-client.ts

@@ -379,32 +379,6 @@ export const verifySession = async (): Promise<boolean> => {
   }
 };
 
-/**
- * Check if the server is running in a containerized (sandbox) environment.
- * This endpoint is unauthenticated so it can be checked before login.
- */
-export const checkSandboxEnvironment = async (): Promise<{
-  isContainerized: boolean;
-  error?: string;
-}> => {
-  try {
-    const response = await fetch(`${getServerUrl()}/api/health/environment`, {
-      method: 'GET',
-    });
-
-    if (!response.ok) {
-      logger.warn('Failed to check sandbox environment');
-      return { isContainerized: false, error: 'Failed to check environment' };
-    }
-
-    const data = await response.json();
-    return { isContainerized: data.isContainerized ?? false };
-  } catch (error) {
-    logger.error('Sandbox environment check failed:', error);
-    return { isContainerized: false, error: 'Network error' };
-  }
-};
-
 type EventType =
   | 'agent:stream'
   | 'auto-mode:event'

apps/ui/src/routes/__root.tsx

@@ -16,28 +16,19 @@ import {
   initApiKey,
   isElectronMode,
   verifySession,
-  checkSandboxEnvironment,
   getServerUrlSync,
   checkExternalServerMode,
   isExternalServerMode,
 } from '@/lib/http-api-client';
 import { Toaster } from 'sonner';
 import { ThemeOption, themeOptions } from '@/config/theme-options';
-import { SandboxRiskDialog } from '@/components/dialogs/sandbox-risk-dialog';
-import { SandboxRejectionScreen } from '@/components/dialogs/sandbox-rejection-screen';
 import { LoadingState } from '@/components/ui/loading-state';
 
 const logger = createLogger('RootLayout');
 
 function RootLayoutContent() {
   const location = useLocation();
-  const {
-    setIpcConnected,
-    currentProject,
-    getEffectiveTheme,
-    skipSandboxWarning,
-    setSkipSandboxWarning,
-  } = useAppStore();
+  const { setIpcConnected, currentProject, getEffectiveTheme } = useAppStore();
   const { setupComplete } = useSetupStore();
   const navigate = useNavigate();
   const [isMounted, setIsMounted] = useState(false);
@@ -52,12 +43,6 @@ function RootLayoutContent() {
   const isSetupRoute = location.pathname === '/setup';
   const isLoginRoute = location.pathname === '/login';
 
-  // Sandbox environment check state
-  type SandboxStatus = 'pending' | 'containerized' | 'needs-confirmation' | 'denied' | 'confirmed';
-  // Always start from pending on a fresh page load so the user sees the prompt
-  // each time the app is launched/refreshed (unless running in a container).
-  const [sandboxStatus, setSandboxStatus] = useState<SandboxStatus>('pending');
-
   // Hidden streamer panel - opens with "\" key
   const handleStreamerPanelShortcut = useCallback((event: KeyboardEvent) => {
     const activeElement = document.activeElement;
@@ -104,73 +89,6 @@ function RootLayoutContent() {
     setIsMounted(true);
   }, []);
 
-  // Check sandbox environment on mount
-  useEffect(() => {
-    // Skip if already decided
-    if (sandboxStatus !== 'pending') {
-      return;
-    }
-
-    const checkSandbox = async () => {
-      try {
-        const result = await checkSandboxEnvironment();
-
-        if (result.isContainerized) {
-          // Running in a container, no warning needed
-          setSandboxStatus('containerized');
-        } else if (skipSandboxWarning) {
-          // User opted to skip the warning, auto-confirm
-          setSandboxStatus('confirmed');
-        } else {
-          // Not containerized, show warning dialog
-          setSandboxStatus('needs-confirmation');
-        }
-      } catch (error) {
-        logger.error('Failed to check environment:', error);
-        // On error, assume not containerized and show warning
-        if (skipSandboxWarning) {
-          setSandboxStatus('confirmed');
-        } else {
-          setSandboxStatus('needs-confirmation');
-        }
-      }
-    };
-
-    checkSandbox();
-  }, [sandboxStatus, skipSandboxWarning]);
-
-  // Handle sandbox risk confirmation
-  const handleSandboxConfirm = useCallback(
-    (skipInFuture: boolean) => {
-      if (skipInFuture) {
-        setSkipSandboxWarning(true);
-      }
-      setSandboxStatus('confirmed');
-    },
-    [setSkipSandboxWarning]
-  );
-
-  // Handle sandbox risk denial
-  const handleSandboxDeny = useCallback(async () => {
-    if (isElectron()) {
-      // In Electron mode, quit the application
-      // Use window.electronAPI directly since getElectronAPI() returns the HTTP client
-      try {
-        const electronAPI = window.electronAPI;
-        if (electronAPI?.quit) {
-          await electronAPI.quit();
-        } else {
-          logger.error('quit() not available on electronAPI');
-        }
-      } catch (error) {
-        logger.error('Failed to quit app:', error);
-      }
-    } else {
-      // In web mode, show rejection screen
-      setSandboxStatus('denied');
-    }
-  }, []);
-
   // Ref to prevent concurrent auth checks from running
   const authCheckRunning = useRef(false);
 
@@ -330,31 +248,11 @@ function RootLayoutContent() {
     }
   }, [deferredTheme]);
 
-  // Show rejection screen if user denied sandbox risk (web mode only)
-  if (sandboxStatus === 'denied' && !isElectron()) {
-    return <SandboxRejectionScreen />;
-  }
-
-  // Show loading while checking sandbox environment
-  if (sandboxStatus === 'pending') {
-    return (
-      <main className="flex h-screen items-center justify-center" data-testid="app-container">
-        <LoadingState message="Checking environment..." />
-      </main>
-    );
-  }
-
   // Show login page (full screen, no sidebar)
   if (isLoginRoute) {
     return (
       <main className="h-screen overflow-hidden" data-testid="app-container">
         <Outlet />
-        {/* Show sandbox dialog on top of login page if needed */}
-        <SandboxRiskDialog
-          open={sandboxStatus === 'needs-confirmation'}
-          onConfirm={handleSandboxConfirm}
-          onDeny={handleSandboxDeny}
-        />
       </main>
     );
   }
@@ -386,12 +284,6 @@ function RootLayoutContent() {
     return (
       <main className="h-screen overflow-hidden" data-testid="app-container">
         <Outlet />
-        {/* Show sandbox dialog on top of setup page if needed */}
-        <SandboxRiskDialog
-          open={sandboxStatus === 'needs-confirmation'}
-          onConfirm={handleSandboxConfirm}
-          onDeny={handleSandboxDeny}
-        />
       </main>
     );
   }
@@ -420,13 +312,6 @@ function RootLayoutContent() {
         }`}
       />
       <Toaster richColors position="bottom-right" />
-
-      {/* Show sandbox dialog if needed */}
-      <SandboxRiskDialog
-        open={sandboxStatus === 'needs-confirmation'}
-        onConfirm={handleSandboxConfirm}
-        onDeny={handleSandboxDeny}
-      />
     </main>
   );
 }

apps/ui/src/store/app-store.ts

@@ -1,9 +1,11 @@
 import { create } from 'zustand';
 import { persist } from 'zustand/middleware';
 import type { Project, TrashedProject } from '@/lib/electron';
+import { createLogger } from '@automaker/utils/logger';
 import type {
   Feature as BaseFeature,
   FeatureImagePath,
+  FeatureTextFilePath,
   ModelAlias,
   PlanningMode,
   AIProfile,
@@ -19,8 +21,10 @@ import type {
 } from '@automaker/types';
 import { getAllCursorModelIds, DEFAULT_PHASE_MODELS } from '@automaker/types';
 
+const logger = createLogger('AppStore');
+
 // Re-export types for convenience
-export type { ThemeMode, ModelAlias };
+export type { ModelAlias };
 
 export type ViewMode =
   | 'welcome'
@@ -460,6 +464,7 @@ export interface AppState {
   // Feature Default Settings
   defaultSkipTests: boolean; // Default value for skip tests when creating new features
   enableDependencyBlocking: boolean; // When true, show blocked badges and warnings for features with incomplete dependencies (default: true)
+  skipVerificationInAutoMode: boolean; // When true, auto-mode grabs features even if dependencies are not verified (only checks they're not running)
 
   // Worktree Settings
   useWorktrees: boolean; // Whether to use git worktree isolation for features (default: false)
@@ -506,8 +511,6 @@ export interface AppState {
 
   // Claude Agent SDK Settings
   autoLoadClaudeMd: boolean; // Auto-load CLAUDE.md files using SDK's settingSources option
-  enableSandboxMode: boolean; // Enable sandbox mode for bash commands (may cause issues on some systems)
-  skipSandboxWarning: boolean; // Skip the sandbox environment warning dialog on startup
 
   // MCP Servers
   mcpServers: MCPServerConfig[]; // List of configured MCP servers for agent use
@@ -749,6 +752,7 @@ export interface AppActions {
   // Feature Default Settings actions
   setDefaultSkipTests: (skip: boolean) => void;
   setEnableDependencyBlocking: (enabled: boolean) => void;
+  setSkipVerificationInAutoMode: (enabled: boolean) => Promise<void>;
 
   // Worktree Settings actions
   setUseWorktrees: (enabled: boolean) => void;
@@ -804,8 +808,6 @@ export interface AppActions {
 
   // Claude Agent SDK Settings actions
   setAutoLoadClaudeMd: (enabled: boolean) => Promise<void>;
-  setEnableSandboxMode: (enabled: boolean) => Promise<void>;
-  setSkipSandboxWarning: (skip: boolean) => Promise<void>;
 
   // Prompt Customization actions
   setPromptCustomization: (customization: PromptCustomization) => Promise<void>;
@@ -1006,6 +1008,7 @@ const initialState: AppState = {
   boardViewMode: 'kanban', // Default to kanban view
   defaultSkipTests: true, // Default to manual verification (tests disabled)
   enableDependencyBlocking: true, // Default to enabled (show dependency blocking UI)
+  skipVerificationInAutoMode: false, // Default to disabled (require dependencies to be verified)
   useWorktrees: false, // Default to disabled (worktree feature is experimental)
   currentWorktreeByProject: {},
   worktreesByProject: {},
@@ -1019,8 +1022,6 @@ const initialState: AppState = {
   enabledCursorModels: getAllCursorModelIds(), // All Cursor models enabled by default
   cursorDefaultModel: 'auto', // Default to auto selection
   autoLoadClaudeMd: false, // Default to disabled (user must opt-in)
-  enableSandboxMode: false, // Default to disabled (can be enabled for additional security)
-  skipSandboxWarning: false, // Default to disabled (show sandbox warning dialog)
   mcpServers: [], // No MCP servers configured by default
   promptCustomization: {}, // Empty by default - all prompts use built-in defaults
   aiProfiles: DEFAULT_AI_PROFILES,
@@ -1574,6 +1575,12 @@ export const useAppStore = create<AppState & AppActions>()(
       // Feature Default Settings actions
       setDefaultSkipTests: (skip) => set({ defaultSkipTests: skip }),
       setEnableDependencyBlocking: (enabled) => set({ enableDependencyBlocking: enabled }),
+      setSkipVerificationInAutoMode: async (enabled) => {
+        set({ skipVerificationInAutoMode: enabled });
+        // Sync to server settings file
+        const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
+        await syncSettingsToServer();
+      },
 
       // Worktree Settings actions
       setUseWorktrees: (enabled) => set({ useWorktrees: enabled }),
@@ -1703,22 +1710,15 @@ export const useAppStore = create<AppState & AppActions>()(
 
       // Claude Agent SDK Settings actions
       setAutoLoadClaudeMd: async (enabled) => {
+        const previous = get().autoLoadClaudeMd;
         set({ autoLoadClaudeMd: enabled });
         // Sync to server settings file
         const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
-        await syncSettingsToServer();
-      },
-      setEnableSandboxMode: async (enabled) => {
-        set({ enableSandboxMode: enabled });
-        // Sync to server settings file
-        const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
-        await syncSettingsToServer();
-      },
-      setSkipSandboxWarning: async (skip) => {
-        set({ skipSandboxWarning: skip });
-        // Sync to server settings file
-        const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
-        await syncSettingsToServer();
+        const ok = await syncSettingsToServer();
+        if (!ok) {
+          logger.error('Failed to sync autoLoadClaudeMd setting to server - reverting');
+          set({ autoLoadClaudeMd: previous });
+        }
       },
       // Prompt Customization actions
       setPromptCustomization: async (customization) => {
@@ -2688,8 +2688,9 @@ export const useAppStore = create<AppState & AppActions>()(
         const current = get().terminalState;
         if (current.tabs.length === 0) {
           // Nothing to save, clear any existing layout
-          const { [projectPath]: _, ...rest } = get().terminalLayoutByProject;
-          set({ terminalLayoutByProject: rest });
+          const next = { ...get().terminalLayoutByProject };
+          delete next[projectPath];
+          set({ terminalLayoutByProject: next });
           return;
         }
 
@@ -2745,8 +2746,9 @@ export const useAppStore = create<AppState & AppActions>()(
       },
 
       clearPersistedTerminalLayout: (projectPath) => {
-        const { [projectPath]: _, ...rest } = get().terminalLayoutByProject;
-        set({ terminalLayoutByProject: rest });
+        const next = { ...get().terminalLayoutByProject };
+        delete next[projectPath];
+        set({ terminalLayoutByProject: next });
       },
 
       // Spec Creation actions
@@ -2995,6 +2997,7 @@ export const useAppStore = create<AppState & AppActions>()(
           // Auto-mode should always default to OFF on app refresh
           defaultSkipTests: state.defaultSkipTests,
           enableDependencyBlocking: state.enableDependencyBlocking,
+          skipVerificationInAutoMode: state.skipVerificationInAutoMode,
           useWorktrees: state.useWorktrees,
           currentWorktreeByProject: state.currentWorktreeByProject,
           worktreesByProject: state.worktreesByProject,
@@ -3007,8 +3010,6 @@ export const useAppStore = create<AppState & AppActions>()(
           enabledCursorModels: state.enabledCursorModels,
           cursorDefaultModel: state.cursorDefaultModel,
           autoLoadClaudeMd: state.autoLoadClaudeMd,
-          enableSandboxMode: state.enableSandboxMode,
-          skipSandboxWarning: state.skipSandboxWarning,
           // MCP settings
           mcpServers: state.mcpServers,
           // Prompt customization