Remove merged tools from the harness on dispose

Teardown detached the bridge and cleared the runner but left the host's
host-provided and extension tools registered (and active) on the harness, so
the model could still call a tool whose runner binding was gone. This is moot at
process exit but matters when an extension calls ctx.shutdown() mid-session,
which disposes the host while the CLI keeps running. disposeNow now restores the
harness to its base tools before the runner goes away.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: rgarcia

packages/cli/src/extensions/host.ts

@@ -340,10 +340,28 @@ export class HarnessExtensionHost {
 		this.disposed = true;
 		this.teardownBridge?.();
 		this.teardownBridge = undefined;
+		// Drop the host + extension tools this host merged into the harness before
+		// the runner goes away: otherwise the model could still call a tool whose
+		// runner binding is gone. (Moot at process exit, but `ctx.shutdown()` from
+		// an extension disposes the host while the CLI keeps running.)
+		await this.removeMergedTools();
 		await this.runner?.emit({ type: "session_shutdown", reason: "quit" });
 		this.runner = undefined;
 	}
 
+	/** Restore the harness to its base tools, removing this host's host+extension tools. */
+	private async removeMergedTools(): Promise<void> {
+		const merged = new Set([...this.hostTools, ...this.extensionTools].map((tool) => tool.name));
+		if (merged.size === 0) return;
+		const base = this.harness.getTools().filter((tool) => !merged.has(tool.name));
+		const active = this.harness
+			.getActiveTools()
+			.map((tool) => tool.name)
+			.filter((name) => !merged.has(name));
+		// Best-effort: a failure here must not block the rest of teardown.
+		await this.harness.setTools(base, active).catch(() => {});
+	}
+
 	private async buildRunner(): Promise<void> {
 		const result = await discoverAndLoadExtensions(this.configuredPaths, this.cwd, this.agentDir);
 		this.loadErrors = result.errors;

packages/cli/test/extensions.test.ts

@@ -148,6 +148,16 @@ describe("HarnessExtensionHost", () => {
 		expect(count()).toBe(1);
 	});
 
+	it("removes its tools from the harness on dispose", async () => {
+		const created = await loadHost();
+		expect(fx!.harness.getTools().map((tool) => tool.name)).toContain("click_visual");
+		// dispose (e.g. via an extension's ctx.shutdown) must not leave the tool
+		// registered+active once its runner binding is gone.
+		await created.dispose();
+		const names = fx!.harness.getTools().map((tool) => tool.name);
+		expect(names).not.toContain("click_visual");
+	});
+
 	it("coalesces a reload requested while another is in flight", async () => {
 		const created = await loadHost();
 		// reload() sets `reloading` synchronously before its first await, so a second