fix: skip EXTRA_BASE scan when workDir is set

Prevents the agent-runner from scanning all subdirectories of the
project as additionalDirectories, which caused SDK crashes.

src/db.ts

@@ -130,9 +130,7 @@ function createSchema(database: Database.Database): void {
 
   // Add work_dir column if it doesn't exist (migration for per-group working directory)
   try {
-    database.exec(
-      `ALTER TABLE registered_groups ADD COLUMN work_dir TEXT`,
-    );
+    database.exec(`ALTER TABLE registered_groups ADD COLUMN work_dir TEXT`);
   } catch {
     /* column already exists */
   }