Remove Smithery config overrides for consistent behavior

Smithery entry point now behaves identically to index.ts:
- No CLI flag config options
- All configuration via config.yaml and env vars
- Same precedence: config.yaml > env vars > defaults

This aligns with the vision of config.yaml as canonical truth.

Also removes unused xcodemake imports from index.ts.

Author: cameroncooke

src/index.ts

@@ -24,9 +24,6 @@ import { getDefaultDebuggerManager } from './utils/debugger/index.ts';
 // Import version
 import { version } from './version.ts';
 
-// Import xcodemake utilities
-import { isXcodemakeEnabled, isXcodemakeAvailable } from './utils/xcodemake.ts';
-
 // Import process for stdout configuration
 import process from 'node:process';
 
@@ -39,22 +36,6 @@ async function main(): Promise<void> {
   try {
     initSentry();
 
-    // Check if xcodemake is enabled and available
-    if (isXcodemakeEnabled()) {
-      log('info', 'xcodemake is enabled, checking if available...');
-      const available = await isXcodemakeAvailable();
-      if (available) {
-        log('info', 'xcodemake is available and will be used for builds');
-      } else {
-        log(
-          'warn',
-          'xcodemake is enabled but could not be made available, falling back to xcodebuild',
-        );
-      }
-    } else {
-      log('debug', 'xcodemake is disabled, using standard xcodebuild');
-    }
-
     // Create the server
     const server = createServer();
 

src/smithery.ts

@@ -4,44 +4,18 @@ import { bootstrapServer } from './server/bootstrap.ts';
 import { createServer } from './server/server.ts';
 import { log } from './utils/logger.ts';
 import { initSentry } from './utils/sentry.ts';
-import type { RuntimeConfigOverrides } from './utils/config-store.ts';
 
-export const configSchema = z.object({
-  incrementalBuildsEnabled: z
-    .boolean()
-    .default(false)
-    .describe('Enable incremental builds via xcodemake (true/false).'),
-  enabledWorkflows: z
-    .string()
-    .default('')
-    .describe('Comma-separated list of workflows to load at startup.'),
-  debug: z.boolean().default(false).describe('Enable debug logging.'),
-});
+// Empty config schema - all configuration comes from config.yaml and env vars
+export const configSchema = z.object({});
 
 export type SmitheryConfig = z.infer<typeof configSchema>;
 
-function parseEnabledWorkflows(value: string): string[] {
-  return value
-    .split(',')
-    .map((name) => name.trim().toLowerCase())
-    .filter(Boolean);
-}
-
-function buildOverrides(config: SmitheryConfig): RuntimeConfigOverrides {
-  return {
-    incrementalBuildsEnabled: config.incrementalBuildsEnabled,
-    debug: config.debug,
-    enabledWorkflows: parseEnabledWorkflows(config.enabledWorkflows),
-  };
-}
-
-export default function createSmitheryServer({ config }: { config: SmitheryConfig }): McpServer {
-  const overrides = buildOverrides(config);
-
+// eslint-disable-next-line @typescript-eslint/no-unused-vars
+export default function createSmitheryServer(options: { config: SmitheryConfig }): McpServer {
   const server = createServer();
   const bootstrapPromise: Promise<void> = (async (): Promise<void> => {
     initSentry();
-    await bootstrapServer(server, { configOverrides: overrides });
+    await bootstrapServer(server);
   })().catch((error) => {
     log(
       'error',