fix(cli): resolve process hang and improve output consistency

- Add process.stdin.destroy() after rl.close() in all interactive commands
  to properly release stdin and allow process to exit cleanly
- Replace raw console.log with logger methods throughout CLI handlers
- Convert manual box drawing to logger.logBox() in daemon.ts
- Standardize menu formatting with logger.info() and logger.dim()
- Improve migration output to only show when migrations actually run

Fixes issue where process would not exit after "Setup complete!" message
due to stdin keeping the event loop alive.

ts/migrations/migration-runner.ts

@@ -34,12 +34,14 @@ export class MigrationRunner {
     let currentConfig = config;
     let anyMigrationsRan = false;
 
-    logger.dim('Checking for required config migrations...');
-
     for (const migration of this.migrations) {
       const shouldRun = await migration.shouldRun(currentConfig);
 
       if (shouldRun) {
+        // Only show "checking" message when we actually need to migrate
+        if (!anyMigrationsRan) {
+          logger.dim('Checking for required config migrations...');
+        }
         logger.info(`Running ${migration.getName()}...`);
         currentConfig = await migration.migrate(currentConfig);
         anyMigrationsRan = true;
@@ -49,7 +51,7 @@ export class MigrationRunner {
     if (anyMigrationsRan) {
       logger.success('Configuration migrations complete');
     } else {
-      logger.dim('No migrations needed');
+      logger.success('config format ok');
     }
 
     return {