refactor: remove MCP permission settings and streamline SDK options for autonomous mode

- Removed MCP permission settings from the application, including related functions and UI components. - Updated SDK options to always bypass permissions and allow unrestricted tool access in autonomous mode. - Adjusted related components and services to reflect the removal of MCP permission configurations, ensuring a cleaner and more efficient codebase.
2026-01-30 06:12:03 +00:00 · 2026-01-03 23:00:20 -05:00
parent 019d6dd7bd
commit e32a82cca5
17 changed files with 36 additions and 361 deletions
--- a/apps/server/src/lib/sdk-options.ts
+++ b/apps/server/src/lib/sdk-options.ts
@@ -252,10 +252,14 @@ export function getModelForUseCase(

 /**
 * Base options that apply to all SDK calls
+ *
+ * AUTONOMOUS MODE: Always bypass permissions and allow dangerous operations
+ * for fully autonomous operation without user prompts.
 */
 function getBaseOptions(): Partial<Options> {
  return {
-    permissionMode: 'acceptEdits',
+    permissionMode: 'bypassPermissions',
+    allowDangerouslySkipPermissions: true,
  };
 }

@@ -276,31 +280,27 @@ interface McpPermissionOptions {
 * Centralizes the logic for determining permission modes and tool restrictions
 * when MCP servers are configured.
 *
+ * AUTONOMOUS MODE: Always bypass permissions for fully autonomous operation.
+ * Always allow unrestricted tools when MCP servers are configured.
+ *
 * @param config - The SDK options config
 * @returns Object with MCP permission settings to spread into final options
 */
 function buildMcpOptions(config: CreateSdkOptionsConfig): McpPermissionOptions {
  const hasMcpServers = config.mcpServers && Object.keys(config.mcpServers).length > 0;
-  // Default to true for autonomous workflow. Security is enforced when adding servers
-  // via the security warning dialog that explains the risks.
-  const mcpAutoApprove = config.mcpAutoApproveTools ?? true;
-  const mcpUnrestricted = config.mcpUnrestrictedTools ?? true;

-  // Determine if we should bypass permissions based on settings
-  const shouldBypassPermissions = hasMcpServers && mcpAutoApprove;
-  // Determine if we should restrict tools (only when no MCP or unrestricted is disabled)
-  const shouldRestrictTools = !hasMcpServers || !mcpUnrestricted;
+  // AUTONOMOUS MODE: Always bypass permissions and allow unrestricted tools
+  // Only restrict tools when no MCP servers are configured
+  const shouldRestrictTools = !hasMcpServers;

  return {
    shouldRestrictTools,
-    // Only include bypass options when MCP is configured and auto-approve is enabled
-    bypassOptions: shouldBypassPermissions
-      ? {
-          permissionMode: 'bypassPermissions' as const,
-          // Required flag when using bypassPermissions mode
-          allowDangerouslySkipPermissions: true,
-        }
-      : {},
+    // AUTONOMOUS MODE: Always include bypass options (though base options already set this)
+    bypassOptions: {
+      permissionMode: 'bypassPermissions' as const,
+      // Required flag when using bypassPermissions mode
+      allowDangerouslySkipPermissions: true,
+    },
    // Include MCP servers if configured
    mcpServerOptions: config.mcpServers ? { mcpServers: config.mcpServers } : {},
  };
@@ -392,12 +392,6 @@ export interface CreateSdkOptionsConfig {

  /** MCP servers to make available to the agent */
  mcpServers?: Record<string, McpServerConfig>;
-
-  /** Auto-approve MCP tool calls without permission prompts */
-  mcpAutoApproveTools?: boolean;
-
-  /** Allow unrestricted tools when MCP servers are enabled */
-  mcpUnrestrictedTools?: boolean;
 }

 // Re-export MCP types from @automaker/types for convenience
@@ -426,10 +420,7 @@ export function createSpecGenerationOptions(config: CreateSdkOptionsConfig): Opt

  return {
    ...getBaseOptions(),
-    // Override permissionMode - spec generation only needs read-only tools
-    // Using "acceptEdits" can cause Claude to write files to unexpected locations
-    // See: https://github.com/AutoMaker-Org/automaker/issues/149
-    permissionMode: 'default',
+    // AUTONOMOUS MODE: Base options already set bypassPermissions and allowDangerouslySkipPermissions
    model: getModelForUseCase('spec', config.model),
    maxTurns: MAX_TURNS.maximum,
    cwd: config.cwd,
@@ -458,8 +449,7 @@ export function createFeatureGenerationOptions(config: CreateSdkOptionsConfig):

  return {
    ...getBaseOptions(),
-    // Override permissionMode - feature generation only needs read-only tools
-    permissionMode: 'default',
+    // AUTONOMOUS MODE: Base options already set bypassPermissions and allowDangerouslySkipPermissions
    model: getModelForUseCase('features', config.model),
    maxTurns: MAX_TURNS.quick,
    cwd: config.cwd,
--- a/apps/server/src/lib/settings-helpers.ts
+++ b/apps/server/src/lib/settings-helpers.ts
@@ -191,41 +191,6 @@ export async function getMCPServersFromSettings(
  }
 }

-/**
- * Get MCP permission settings from global settings.
- *
- * @param settingsService - Optional settings service instance
- * @param logPrefix - Prefix for log messages (e.g., '[AgentService]')
- * @returns Promise resolving to MCP permission settings
- */
-export async function getMCPPermissionSettings(
-  settingsService?: SettingsService | null,
-  logPrefix = '[SettingsHelper]'
-): Promise<{ mcpAutoApproveTools: boolean; mcpUnrestrictedTools: boolean }> {
-  // Default to true for autonomous workflow. Security is enforced when adding servers
-  // via the security warning dialog that explains the risks.
-  const defaults = { mcpAutoApproveTools: true, mcpUnrestrictedTools: true };
-
-  if (!settingsService) {
-    return defaults;
-  }
-
-  try {
-    const globalSettings = await settingsService.getGlobalSettings();
-    const result = {
-      mcpAutoApproveTools: globalSettings.mcpAutoApproveTools ?? true,
-      mcpUnrestrictedTools: globalSettings.mcpUnrestrictedTools ?? true,
-    };
-    logger.info(
-      `${logPrefix} MCP permission settings: autoApprove=${result.mcpAutoApproveTools}, unrestricted=${result.mcpUnrestrictedTools}`
-    );
-    return result;
-  } catch (error) {
-    logger.error(`${logPrefix} Failed to load MCP permission settings:`, error);
-    return defaults;
-  }
-}
-
 /**
 * Convert a settings MCPServerConfig to SDK McpServerConfig format.
 * Validates required fields and throws informative errors if missing.
--- a/apps/server/src/providers/claude-provider.ts
+++ b/apps/server/src/providers/claude-provider.ts
@@ -63,20 +63,13 @@ export class ClaudeProvider extends BaseProvider {
    } = options;

    // Build Claude SDK options
-    // MCP permission logic - determines how to handle tool permissions when MCP servers are configured.
-    // This logic mirrors buildMcpOptions() in sdk-options.ts but is applied here since
-    // the provider is the final point where SDK options are constructed.
+    // AUTONOMOUS MODE: Always bypass permissions for fully autonomous operation
    const hasMcpServers = options.mcpServers && Object.keys(options.mcpServers).length > 0;
-    // Default to true for autonomous workflow. Security is enforced when adding servers
-    // via the security warning dialog that explains the risks.
-    const mcpAutoApprove = options.mcpAutoApproveTools ?? true;
-    const mcpUnrestricted = options.mcpUnrestrictedTools ?? true;
    const defaultTools = ['Read', 'Write', 'Edit', 'Glob', 'Grep', 'Bash', 'WebSearch', 'WebFetch'];

-    // Determine permission mode based on settings
-    const shouldBypassPermissions = hasMcpServers && mcpAutoApprove;
-    // Determine if we should restrict tools (only when no MCP or unrestricted is disabled)
-    const shouldRestrictTools = !hasMcpServers || !mcpUnrestricted;
+    // AUTONOMOUS MODE: Always bypass permissions and allow unrestricted tools
+    // Only restrict tools when no MCP servers are configured
+    const shouldRestrictTools = !hasMcpServers;

    const sdkOptions: Options = {
      model,
@@ -88,10 +81,9 @@ export class ClaudeProvider extends BaseProvider {
      // Only restrict tools if explicitly set OR (no MCP / unrestricted disabled)
      ...(allowedTools && shouldRestrictTools && { allowedTools }),
      ...(!allowedTools && shouldRestrictTools && { allowedTools: defaultTools }),
-      // When MCP servers are configured and auto-approve is enabled, use bypassPermissions
-      permissionMode: shouldBypassPermissions ? 'bypassPermissions' : 'default',
-      // Required when using bypassPermissions mode
-      ...(shouldBypassPermissions && { allowDangerouslySkipPermissions: true }),
+      // AUTONOMOUS MODE: Always bypass permissions and allow dangerous operations
+      permissionMode: 'bypassPermissions',
+      allowDangerouslySkipPermissions: true,
      abortController,
      // Resume existing SDK session if we have a session ID
      ...(sdkSessionId && conversationHistory && conversationHistory.length > 0
--- a/apps/server/src/routes/enhance-prompt/routes/enhance.ts
+++ b/apps/server/src/routes/enhance-prompt/routes/enhance.ts
@@ -164,7 +164,9 @@ export function createEnhanceHandler(
          systemPrompt,
          maxTurns: 1,
          allowedTools: [],
-          permissionMode: 'acceptEdits',
+          // AUTONOMOUS MODE: Always bypass permissions
+          permissionMode: 'bypassPermissions',
+          allowDangerouslySkipPermissions: true,
        },
      });

--- a/apps/server/src/routes/features/routes/generate-title.ts
+++ b/apps/server/src/routes/features/routes/generate-title.ts
@@ -96,7 +96,9 @@ export function createGenerateTitleHandler(): (req: Request, res: Response) => P
          systemPrompt: SYSTEM_PROMPT,
          maxTurns: 1,
          allowedTools: [],
-          permissionMode: 'acceptEdits',
+          // AUTONOMOUS MODE: Always bypass permissions
+          permissionMode: 'bypassPermissions',
+          allowDangerouslySkipPermissions: true,
        },
      });

--- a/apps/server/src/services/agent-service.ts
+++ b/apps/server/src/services/agent-service.ts
@@ -23,7 +23,6 @@ import {
  getEnableSandboxModeSetting,
  filterClaudeMdFromContext,
  getMCPServersFromSettings,
-  getMCPPermissionSettings,
  getPromptCustomization,
 } from '../lib/settings-helpers.js';

@@ -235,9 +234,6 @@ export class AgentService {
      // Load MCP servers from settings (global setting only)
      const mcpServers = await getMCPServersFromSettings(this.settingsService, '[AgentService]');

-      // Load MCP permission settings (global setting only)
-      const mcpPermissions = await getMCPPermissionSettings(this.settingsService, '[AgentService]');
-
      // Load project context files (CLAUDE.md, CODE_QUALITY.md, etc.)
      const contextResult = await loadContextFiles({
        projectPath: effectiveWorkDir,
@@ -264,8 +260,6 @@ export class AgentService {
        autoLoadClaudeMd,
        enableSandboxMode,
        mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
-        mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
-        mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
      });

      // Extract model, maxTurns, and allowedTools from SDK options
@@ -290,8 +284,6 @@ export class AgentService {
        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
-        mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools, // Pass MCP auto-approve setting
-        mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools, // Pass MCP unrestricted tools setting
      };

      // Build prompt content with images
--- a/apps/server/src/services/auto-mode-service.ts
+++ b/apps/server/src/services/auto-mode-service.ts
@@ -38,7 +38,6 @@ import {
  getEnableSandboxModeSetting,
  filterClaudeMdFromContext,
  getMCPServersFromSettings,
-  getMCPPermissionSettings,
  getPromptCustomization,
 } from '../lib/settings-helpers.js';

@@ -2003,9 +2002,6 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
    // Load MCP servers from settings (global setting only)
    const mcpServers = await getMCPServersFromSettings(this.settingsService, '[AutoMode]');

-    // Load MCP permission settings (global setting only)
-    const mcpPermissions = await getMCPPermissionSettings(this.settingsService, '[AutoMode]');
-
    // Build SDK options using centralized configuration for feature implementation
    const sdkOptions = createAutoModeOptions({
      cwd: workDir,
@@ -2014,8 +2010,6 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
      autoLoadClaudeMd,
      enableSandboxMode,
      mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
-      mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
-      mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
    });

    // Extract model, maxTurns, and allowedTools from SDK options
@@ -2058,8 +2052,6 @@ This mock response was generated because AUTOMAKER_MOCK_AGENT=true was set.
      settingSources: sdkOptions.settingSources,
      sandbox: sdkOptions.sandbox, // Pass sandbox configuration
      mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined, // Pass MCP servers configuration
-      mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools, // Pass MCP auto-approve setting
-      mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools, // Pass MCP unrestricted tools setting
    };

    // Execute via provider
@@ -2291,8 +2283,6 @@ After generating the revised spec, output:
                        allowedTools: allowedTools,
                        abortController,
                        mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
-                        mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
-                        mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
                      });

                      let revisionText = '';
@@ -2431,8 +2421,6 @@ After generating the revised spec, output:
                    allowedTools: allowedTools,
                    abortController,
                    mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
-                    mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
-                    mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
                  });

                  let taskOutput = '';
@@ -2523,8 +2511,6 @@ Implement all the changes described in the plan above.`;
                  allowedTools: allowedTools,
                  abortController,
                  mcpServers: Object.keys(mcpServers).length > 0 ? mcpServers : undefined,
-                  mcpAutoApproveTools: mcpPermissions.mcpAutoApproveTools,
-                  mcpUnrestrictedTools: mcpPermissions.mcpUnrestrictedTools,
                });

                for await (const msg of continuationStream) {
--- a/apps/server/tests/unit/lib/settings-helpers.test.ts
+++ b/apps/server/tests/unit/lib/settings-helpers.test.ts
@@ -1,5 +1,5 @@
 import { describe, it, expect, vi, beforeEach } from 'vitest';
-import { getMCPServersFromSettings, getMCPPermissionSettings } from '@/lib/settings-helpers.js';
+import { getMCPServersFromSettings } from '@/lib/settings-helpers.js';
 import type { SettingsService } from '@/services/settings-service.js';

 // Mock the logger
@@ -286,93 +286,4 @@ describe('settings-helpers.ts', () => {
      });
    });
  });
-
-  describe('getMCPPermissionSettings', () => {
-    beforeEach(() => {
-      vi.clearAllMocks();
-    });
-
-    it('should return defaults when settingsService is null', async () => {
-      const result = await getMCPPermissionSettings(null);
-      expect(result).toEqual({
-        mcpAutoApproveTools: true,
-        mcpUnrestrictedTools: true,
-      });
-    });
-
-    it('should return defaults when settingsService is undefined', async () => {
-      const result = await getMCPPermissionSettings(undefined);
-      expect(result).toEqual({
-        mcpAutoApproveTools: true,
-        mcpUnrestrictedTools: true,
-      });
-    });
-
-    it('should return settings from service', async () => {
-      const mockSettingsService = {
-        getGlobalSettings: vi.fn().mockResolvedValue({
-          mcpAutoApproveTools: false,
-          mcpUnrestrictedTools: false,
-        }),
-      } as unknown as SettingsService;
-
-      const result = await getMCPPermissionSettings(mockSettingsService);
-      expect(result).toEqual({
-        mcpAutoApproveTools: false,
-        mcpUnrestrictedTools: false,
-      });
-    });
-
-    it('should default to true when settings are undefined', async () => {
-      const mockSettingsService = {
-        getGlobalSettings: vi.fn().mockResolvedValue({}),
-      } as unknown as SettingsService;
-
-      const result = await getMCPPermissionSettings(mockSettingsService);
-      expect(result).toEqual({
-        mcpAutoApproveTools: true,
-        mcpUnrestrictedTools: true,
-      });
-    });
-
-    it('should handle mixed settings', async () => {
-      const mockSettingsService = {
-        getGlobalSettings: vi.fn().mockResolvedValue({
-          mcpAutoApproveTools: true,
-          mcpUnrestrictedTools: false,
-        }),
-      } as unknown as SettingsService;
-
-      const result = await getMCPPermissionSettings(mockSettingsService);
-      expect(result).toEqual({
-        mcpAutoApproveTools: true,
-        mcpUnrestrictedTools: false,
-      });
-    });
-
-    it('should return defaults and log error on exception', async () => {
-      const mockSettingsService = {
-        getGlobalSettings: vi.fn().mockRejectedValue(new Error('Settings error')),
-      } as unknown as SettingsService;
-
-      const result = await getMCPPermissionSettings(mockSettingsService, '[Test]');
-      expect(result).toEqual({
-        mcpAutoApproveTools: true,
-        mcpUnrestrictedTools: true,
-      });
-      // Logger will be called with error, but we don't need to assert it
-    });
-
-    it('should use custom log prefix', async () => {
-      const mockSettingsService = {
-        getGlobalSettings: vi.fn().mockResolvedValue({
-          mcpAutoApproveTools: true,
-          mcpUnrestrictedTools: true,
-        }),
-      } as unknown as SettingsService;
-
-      await getMCPPermissionSettings(mockSettingsService, '[CustomPrefix]');
-      // Logger will be called with custom prefix, but we don't need to assert it
-    });
-  });
 });
--- a/apps/ui/src/components/views/settings-view/mcp-servers/components/index.ts
+++ b/apps/ui/src/components/views/settings-view/mcp-servers/components/index.ts
@@ -1,4 +1,3 @@
 export { MCPServerHeader } from './mcp-server-header';
-export { MCPPermissionSettings } from './mcp-permission-settings';
 export { MCPToolsWarning } from './mcp-tools-warning';
 export { MCPServerCard } from './mcp-server-card';
--- a/apps/ui/src/components/views/settings-view/mcp-servers/components/mcp-permission-settings.tsx
+++ b/apps/ui/src/components/views/settings-view/mcp-servers/components/mcp-permission-settings.tsx
@@ -1,96 +0,0 @@
-import { ShieldAlert } from 'lucide-react';
-import { Label } from '@/components/ui/label';
-import { Switch } from '@/components/ui/switch';
-import { syncSettingsToServer } from '@/hooks/use-settings-migration';
-import { cn } from '@/lib/utils';
-
-interface MCPPermissionSettingsProps {
-  mcpAutoApproveTools: boolean;
-  mcpUnrestrictedTools: boolean;
-  onAutoApproveChange: (checked: boolean) => void;
-  onUnrestrictedChange: (checked: boolean) => void;
-}
-
-export function MCPPermissionSettings({
-  mcpAutoApproveTools,
-  mcpUnrestrictedTools,
-  onAutoApproveChange,
-  onUnrestrictedChange,
-}: MCPPermissionSettingsProps) {
-  const hasAnyEnabled = mcpAutoApproveTools || mcpUnrestrictedTools;
-
-  return (
-    <div className="px-6 py-4 border-b border-border/50 bg-muted/20">
-      <div className="space-y-4">
-        <div className="flex items-start gap-3">
-          <Switch
-            id="mcp-auto-approve"
-            checked={mcpAutoApproveTools}
-            onCheckedChange={async (checked) => {
-              onAutoApproveChange(checked);
-              await syncSettingsToServer();
-            }}
-            data-testid="mcp-auto-approve-toggle"
-            className="mt-0.5"
-          />
-          <div className="space-y-1 flex-1">
-            <Label htmlFor="mcp-auto-approve" className="text-sm font-medium cursor-pointer">
-              Auto-approve MCP tool calls
-            </Label>
-            <p className="text-xs text-muted-foreground">
-              When enabled, the AI agent can use MCP tools without permission prompts.
-            </p>
-            {mcpAutoApproveTools && (
-              <p className="text-xs text-amber-600 flex items-center gap-1 mt-1">
-                <ShieldAlert className="h-3 w-3" />
-                Bypasses normal permission checks
-              </p>
-            )}
-          </div>
-        </div>
-
-        <div className="flex items-start gap-3">
-          <Switch
-            id="mcp-unrestricted"
-            checked={mcpUnrestrictedTools}
-            onCheckedChange={async (checked) => {
-              onUnrestrictedChange(checked);
-              await syncSettingsToServer();
-            }}
-            data-testid="mcp-unrestricted-toggle"
-            className="mt-0.5"
-          />
-          <div className="space-y-1 flex-1">
-            <Label htmlFor="mcp-unrestricted" className="text-sm font-medium cursor-pointer">
-              Unrestricted tool access
-            </Label>
-            <p className="text-xs text-muted-foreground">
-              When enabled, the AI agent can use any tool, not just the default set.
-            </p>
-            {mcpUnrestrictedTools && (
-              <p className="text-xs text-amber-600 flex items-center gap-1 mt-1">
-                <ShieldAlert className="h-3 w-3" />
-                Agent has full tool access including file writes and bash
-              </p>
-            )}
-          </div>
-        </div>
-
-        {hasAnyEnabled && (
-          <div
-            className={cn(
-              'rounded-md border border-amber-500/30 bg-amber-500/10 p-3 mt-2',
-              'text-xs text-amber-700 dark:text-amber-400'
-            )}
-          >
-            <p className="font-medium mb-1">Security Note</p>
-            <p>
-              These settings reduce security restrictions for MCP tool usage. Only enable if you
-              trust all configured MCP servers.
-            </p>
-          </div>
-        )}
-      </div>
-    </div>
-  );
-}
--- a/apps/ui/src/components/views/settings-view/mcp-servers/hooks/use-mcp-servers.ts
+++ b/apps/ui/src/components/views/settings-view/mcp-servers/hooks/use-mcp-servers.ts
@@ -21,16 +21,7 @@ interface PendingServerData {
 }

 export function useMCPServers() {
-  const {
-    mcpServers,
-    addMCPServer,
-    updateMCPServer,
-    removeMCPServer,
-    mcpAutoApproveTools,
-    mcpUnrestrictedTools,
-    setMcpAutoApproveTools,
-    setMcpUnrestrictedTools,
-  } = useAppStore();
+  const { mcpServers, addMCPServer, updateMCPServer, removeMCPServer } = useAppStore();

  // State
  const [isAddDialogOpen, setIsAddDialogOpen] = useState(false);
@@ -938,10 +929,6 @@ export function useMCPServers() {
  return {
    // Store state
    mcpServers,
-    mcpAutoApproveTools,
-    mcpUnrestrictedTools,
-    setMcpAutoApproveTools,
-    setMcpUnrestrictedTools,

    // Dialog state
    isAddDialogOpen,
--- a/apps/ui/src/components/views/settings-view/mcp-servers/mcp-servers-section.tsx
+++ b/apps/ui/src/components/views/settings-view/mcp-servers/mcp-servers-section.tsx
@@ -1,12 +1,7 @@
 import { Plug } from 'lucide-react';
 import { cn } from '@/lib/utils';
 import { useMCPServers } from './hooks';
-import {
-  MCPServerHeader,
-  MCPPermissionSettings,
-  MCPToolsWarning,
-  MCPServerCard,
-} from './components';
+import { MCPServerHeader, MCPToolsWarning, MCPServerCard } from './components';
 import {
  AddEditServerDialog,
  DeleteServerDialog,
@@ -20,10 +15,6 @@ export function MCPServersSection() {
  const {
    // Store state
    mcpServers,
-    mcpAutoApproveTools,
-    mcpUnrestrictedTools,
-    setMcpAutoApproveTools,
-    setMcpUnrestrictedTools,

    // Dialog state
    isAddDialogOpen,
@@ -98,15 +89,6 @@ export function MCPServersSection() {
        onAdd={handleOpenAddDialog}
      />

-      {mcpServers.length > 0 && (
-        <MCPPermissionSettings
-          mcpAutoApproveTools={mcpAutoApproveTools}
-          mcpUnrestrictedTools={mcpUnrestrictedTools}
-          onAutoApproveChange={setMcpAutoApproveTools}
-          onUnrestrictedChange={setMcpUnrestrictedTools}
-        />
-      )}
-
      {showToolsWarning && <MCPToolsWarning totalTools={totalToolsCount} />}

      <div className="p-6">
--- a/apps/ui/src/hooks/use-settings-migration.ts
+++ b/apps/ui/src/hooks/use-settings-migration.ts
@@ -230,8 +230,6 @@ export async function syncSettingsToServer(): Promise<boolean> {
      keyboardShortcuts: state.keyboardShortcuts,
      aiProfiles: state.aiProfiles,
      mcpServers: state.mcpServers,
-      mcpAutoApproveTools: state.mcpAutoApproveTools,
-      mcpUnrestrictedTools: state.mcpUnrestrictedTools,
      promptCustomization: state.promptCustomization,
      projects: state.projects,
      trashedProjects: state.trashedProjects,
@@ -336,12 +334,10 @@ export async function loadMCPServersFromServer(): Promise<boolean> {
    }

    const mcpServers = result.settings.mcpServers || [];
-    const mcpAutoApproveTools = result.settings.mcpAutoApproveTools ?? true;
-    const mcpUnrestrictedTools = result.settings.mcpUnrestrictedTools ?? true;

    // Clear existing and add all from server
    // We need to update the store directly since we can't use hooks here
-    useAppStore.setState({ mcpServers, mcpAutoApproveTools, mcpUnrestrictedTools });
+    useAppStore.setState({ mcpServers });

    console.log(`[Settings Load] Loaded ${mcpServers.length} MCP servers from server`);
    return true;
--- a/apps/ui/src/lib/http-api-client.ts
+++ b/apps/ui/src/lib/http-api-client.ts
@@ -1438,8 +1438,6 @@ export class HttpApiClient implements ElectronAPI {
          headers?: Record<string, string>;
          enabled?: boolean;
        }>;
-        mcpAutoApproveTools?: boolean;
-        mcpUnrestrictedTools?: boolean;
      };
      error?: string;
    }> => this.get('/api/settings/global'),
--- a/apps/ui/src/store/app-store.ts
+++ b/apps/ui/src/store/app-store.ts
@@ -491,8 +491,6 @@ export interface AppState {

  // MCP Servers
  mcpServers: MCPServerConfig[]; // List of configured MCP servers for agent use
-  mcpAutoApproveTools: boolean; // Auto-approve MCP tool calls without permission prompts
-  mcpUnrestrictedTools: boolean; // Allow unrestricted tools when MCP servers are enabled

  // Prompt Customization
  promptCustomization: PromptCustomization; // Custom prompts for Auto Mode, Agent, Backlog Plan, Enhancement
@@ -777,8 +775,6 @@ export interface AppActions {
  setAutoLoadClaudeMd: (enabled: boolean) => Promise<void>;
  setEnableSandboxMode: (enabled: boolean) => Promise<void>;
  setSkipSandboxWarning: (skip: boolean) => Promise<void>;
-  setMcpAutoApproveTools: (enabled: boolean) => Promise<void>;
-  setMcpUnrestrictedTools: (enabled: boolean) => Promise<void>;

  // Prompt Customization actions
  setPromptCustomization: (customization: PromptCustomization) => Promise<void>;
@@ -980,8 +976,6 @@ const initialState: AppState = {
  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
-  mcpAutoApproveTools: true, // Default to enabled - bypass permission prompts for MCP tools
-  mcpUnrestrictedTools: true, // Default to enabled - don't filter allowedTools when MCP enabled
  promptCustomization: {}, // Empty by default - all prompts use built-in defaults
  aiProfiles: DEFAULT_AI_PROFILES,
  projectAnalysis: null,
@@ -1632,19 +1626,6 @@ export const useAppStore = create<AppState & AppActions>()(
        const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
        await syncSettingsToServer();
      },
-      setMcpAutoApproveTools: async (enabled) => {
-        set({ mcpAutoApproveTools: enabled });
-        // Sync to server settings file
-        const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
-        await syncSettingsToServer();
-      },
-      setMcpUnrestrictedTools: async (enabled) => {
-        set({ mcpUnrestrictedTools: enabled });
-        // Sync to server settings file
-        const { syncSettingsToServer } = await import('@/hooks/use-settings-migration');
-        await syncSettingsToServer();
-      },
-
      // Prompt Customization actions
      setPromptCustomization: async (customization) => {
        set({ promptCustomization: customization });
@@ -2933,8 +2914,6 @@ export const useAppStore = create<AppState & AppActions>()(
          skipSandboxWarning: state.skipSandboxWarning,
          // MCP settings
          mcpServers: state.mcpServers,
-          mcpAutoApproveTools: state.mcpAutoApproveTools,
-          mcpUnrestrictedTools: state.mcpUnrestrictedTools,
          // Prompt customization
          promptCustomization: state.promptCustomization,
          // Profiles and sessions
--- a/libs/types/src/provider.ts
+++ b/libs/types/src/provider.ts
@@ -71,8 +71,6 @@ export interface ExecuteOptions {
  maxTurns?: number;
  allowedTools?: string[];
  mcpServers?: Record<string, McpServerConfig>;
-  mcpAutoApproveTools?: boolean; // Auto-approve MCP tool calls without permission prompts
-  mcpUnrestrictedTools?: boolean; // Allow unrestricted tools when MCP servers are enabled
  abortController?: AbortController;
  conversationHistory?: ConversationMessage[]; // Previous messages for context
  sdkSessionId?: string; // Claude SDK session ID for resuming conversations
--- a/libs/types/src/settings.ts
+++ b/libs/types/src/settings.ts
@@ -359,10 +359,6 @@ export interface GlobalSettings {
  // MCP Server Configuration
  /** List of configured MCP servers for agent use */
  mcpServers: MCPServerConfig[];
-  /** Auto-approve MCP tool calls without permission prompts (uses bypassPermissions mode) */
-  mcpAutoApproveTools?: boolean;
-  /** Allow unrestricted tools when MCP servers are enabled (don't filter allowedTools) */
-  mcpUnrestrictedTools?: boolean;

  // Prompt Customization
  /** Custom prompts for Auto Mode, Agent Runner, Backlog Planning, and Enhancements */
@@ -535,10 +531,6 @@ export const DEFAULT_GLOBAL_SETTINGS: GlobalSettings = {
  enableSandboxMode: false,
  skipSandboxWarning: false,
  mcpServers: [],
-  // Default to true for autonomous workflow. Security is enforced when adding servers
-  // via the security warning dialog that explains the risks.
-  mcpAutoApproveTools: true,
-  mcpUnrestrictedTools: true,
 };

 /** Default credentials (empty strings - user must provide API keys) */