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.

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

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) {