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.

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

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) */