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

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

@@ -20,7 +20,6 @@ import { PathNotAllowedError } from '@automaker/platform';
 import type { SettingsService } from './settings-service.js';
 import {
   getAutoLoadClaudeMdSetting,
-  getEnableSandboxModeSetting,
   filterClaudeMdFromContext,
   getMCPServersFromSettings,
   getPromptCustomization,
@@ -232,12 +231,6 @@ export class AgentService {
         '[AgentService]'
       );
 
-      // Load enableSandboxMode setting (global setting only)
-      const enableSandboxMode = await getEnableSandboxModeSetting(
-        this.settingsService,
-        '[AgentService]'
-      );
-
       // Load MCP servers from settings (global setting only)
       const mcpServers = await getMCPServersFromSettings(this.settingsService, '[AgentService]');
 
@@ -267,7 +260,6 @@ export class AgentService {
         systemPrompt: combinedSystemPrompt,
         abortController: session.abortController!,
         autoLoadClaudeMd,
-        enableSandboxMode,
         thinkingLevel: effectiveThinkingLevel, // Pass thinking level for Claude models
         mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
       });
@@ -291,7 +283,6 @@ export class AgentService {
         abortController: session.abortController!,
         conversationHistory: conversationHistory.length > 0 ? conversationHistory : undefined,
         settingSources: sdkOptions.settingSources,
-        sandbox: sdkOptions.sandbox, // Pass sandbox configuration
         sdkSessionId: session.sdkSessionId, // Pass SDK session ID for resuming
         mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined, // Pass MCP servers configuration
       };

apps/server/src/services/auto-mode-service.ts

@@ -47,7 +47,6 @@ import type { SettingsService } from './settings-service.js';
 import { pipelineService, PipelineService } from './pipeline-service.js';
 import {
   getAutoLoadClaudeMdSetting,
-  getEnableSandboxModeSetting,
   filterClaudeMdFromContext,
   getMCPServersFromSettings,
   getPromptCustomization,
@@ -1314,7 +1313,6 @@ Format your response as a structured markdown document.`;
         allowedTools: sdkOptions.allowedTools as string[],
         abortController,
         settingSources: sdkOptions.settingSources,
-        sandbox: sdkOptions.sandbox, // Pass sandbox configuration
         thinkingLevel: analysisThinkingLevel, // Pass thinking level
       };
 
@@ -1784,9 +1782,13 @@ Format your response as a structured markdown document.`;
       // Apply dependency-aware ordering
       const { orderedFeatures } = resolveDependencies(pendingFeatures);
 
+      // Get skipVerificationInAutoMode setting
+      const settings = await this.settingsService?.getGlobalSettings();
+      const skipVerification = settings?.skipVerificationInAutoMode ?? false;
+
       // Filter to only features with satisfied dependencies
       const readyFeatures = orderedFeatures.filter((feature: Feature) =>
-        areDependenciesSatisfied(feature, allFeatures)
+        areDependenciesSatisfied(feature, allFeatures, { skipVerification })
       );
 
       return readyFeatures;
@@ -2062,9 +2064,6 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
         ? options.autoLoadClaudeMd
         : await getAutoLoadClaudeMdSetting(finalProjectPath, this.settingsService, '[AutoMode]');
 
-    // Load enableSandboxMode setting (global setting only)
-    const enableSandboxMode = await getEnableSandboxModeSetting(this.settingsService, '[AutoMode]');
-
     // Load MCP servers from settings (global setting only)
     const mcpServers = await getMCPServersFromSettings(this.settingsService, '[AutoMode]');
 
@@ -2076,7 +2075,6 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
       model: model,
       abortController,
       autoLoadClaudeMd,
-      enableSandboxMode,
       mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
       thinkingLevel: options?.thinkingLevel,
     });
@@ -2119,7 +2117,6 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
       abortController,
       systemPrompt: sdkOptions.systemPrompt,
       settingSources: sdkOptions.settingSources,
-      sandbox: sdkOptions.sandbox, // Pass sandbox configuration
       mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined, // Pass MCP servers configuration
       thinkingLevel: options?.thinkingLevel, // Pass thinking level for extended thinking
     };
@@ -2202,9 +2199,23 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
       }, WRITE_DEBOUNCE_MS);
     };
 
+    // Heartbeat logging so "silent" model calls are visible.
+    // Some runs can take a while before the first streamed message arrives.
+    const streamStartTime = Date.now();
+    let receivedAnyStreamMessage = false;
+    const STREAM_HEARTBEAT_MS = 15_000;
+    const streamHeartbeat = setInterval(() => {
+      if (receivedAnyStreamMessage) return;
+      const elapsedSeconds = Math.round((Date.now() - streamStartTime) / 1000);
+      logger.info(
+        `Waiting for first model response for feature ${featureId} (${elapsedSeconds}s elapsed)...`
+      );
+    }, STREAM_HEARTBEAT_MS);
+
     // Wrap stream processing in try/finally to ensure timeout cleanup on any error/abort
     try {
       streamLoop: for await (const msg of stream) {
+        receivedAnyStreamMessage = true;
         // Log raw stream event for debugging
         appendRawEvent(msg);
 
@@ -2721,6 +2732,7 @@ Implement all the changes described in the plan above.`;
         }
       }
     } finally {
+      clearInterval(streamHeartbeat);
       // ALWAYS clear pending timeouts to prevent memory leaks
       // This runs on success, error, or abort
       if (writeTimeout) {

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

@@ -153,14 +153,6 @@ export class SettingsService {
     const storedVersion = settings.version || 1;
     let needsSave = false;
 
-    // Migration v1 -> v2: Force enableSandboxMode to false for existing users
-    // Sandbox mode can cause issues on some systems, so we're disabling it by default
-    if (storedVersion < 2) {
-      logger.info('Migrating settings from v1 to v2: disabling sandbox mode');
-      result.enableSandboxMode = false;
-      needsSave = true;
-    }
-
     // Migration v2 -> v3: Convert string phase models to PhaseModelEntry objects
     // Note: migratePhaseModels() handles the actual conversion for both v1 and v2 formats
     if (storedVersion < 3) {
@@ -537,6 +529,10 @@ export class SettingsService {
           appState.enableDependencyBlocking !== undefined
             ? (appState.enableDependencyBlocking as boolean)
             : true,
+        skipVerificationInAutoMode:
+          appState.skipVerificationInAutoMode !== undefined
+            ? (appState.skipVerificationInAutoMode as boolean)
+            : false,
         useWorktrees: (appState.useWorktrees as boolean) || false,
         showProfilesOnly: (appState.showProfilesOnly as boolean) || false,
         defaultPlanningMode: