diff --git a/src/headless.ts b/src/headless.ts
index 59026a2..1ad9d1a 100644
--- a/src/headless.ts
+++ b/src/headless.ts
@@ -65,6 +65,12 @@ export async function handleHeadlessCommand(
     allowPositionals: true,
   });
 
+  // Set tool filter if provided (controls which tools are loaded)
+  if (values.tools !== undefined) {
+    const { toolFilter } = await import("./tools/filter");
+    toolFilter.setEnabledTools(values.tools as string);
+  }
+
   // Get prompt from either positional args or stdin
   let prompt = positionals.slice(2).join(" ");
 
diff --git a/src/tools/filter.ts b/src/tools/filter.ts
index b8b3daf..4d6c9f4 100644
--- a/src/tools/filter.ts
+++ b/src/tools/filter.ts
@@ -62,5 +62,20 @@ class ToolFilterManager {
   }
 }
 
-// Singleton instance
-export const toolFilter = new ToolFilterManager();
+// Use globalThis to ensure singleton across bundle
+// This prevents Bun's bundler from creating duplicate instances
+const FILTER_KEY = Symbol.for("@letta/toolFilter");
+
+type GlobalWithFilter = typeof globalThis & {
+  [key: symbol]: ToolFilterManager;
+};
+
+function getFilter(): ToolFilterManager {
+  const global = globalThis as GlobalWithFilter;
+  if (!global[FILTER_KEY]) {
+    global[FILTER_KEY] = new ToolFilterManager();
+  }
+  return global[FILTER_KEY];
+}
+
+export const toolFilter = getFilter();