Refactor subagent tool, fix custom tool discovery, fix JSON mode stdout flush

Breaking changes:
- Custom tools now require index.ts entry point in subdirectory
  (e.g., tools/mytool/index.ts instead of tools/mytool.ts)

Subagent tool improvements:
- Refactored to use Message[] from ai package instead of custom types
- Extracted agent discovery to separate agents.ts module
- Added parallel mode streaming (shows progress from all tasks)
- Added turn count to usage stats footer
- Removed redundant Query section from scout output

Fixes:
- JSON mode stdout flush: Fixed race condition where pi --mode json
  could exit before all output was written, causing consumers to
  miss final events

Also:
- Added signal/timeout support to pi.exec() for custom tools and hooks
- Renamed pi-pods bin to avoid conflict with pi

packages/coding-agent/src/core/hooks/runner.ts

@@ -6,6 +6,7 @@ import { spawn } from "node:child_process";
 import type { LoadedHook, SendHandler } from "./loader.js";
 import type {
 	BranchEventResult,
+	ExecOptions,
 	ExecResult,
 	HookError,
 	HookEvent,
@@ -28,13 +29,45 @@ export type HookErrorListener = (error: HookError) => void;
 
 /**
  * Execute a command and return stdout/stderr/code.
+ * Supports cancellation via AbortSignal and timeout.
  */
-async function exec(command: string, args: string[], cwd: string): Promise<ExecResult> {
+async function exec(command: string, args: string[], cwd: string, options?: ExecOptions): Promise<ExecResult> {
 	return new Promise((resolve) => {
 		const proc = spawn(command, args, { cwd, shell: false });
 
 		let stdout = "";
 		let stderr = "";
+		let killed = false;
+		let timeoutId: NodeJS.Timeout | undefined;
+
+		const killProcess = () => {
+			if (!killed) {
+				killed = true;
+				proc.kill("SIGTERM");
+				// Force kill after 5 seconds if SIGTERM doesn't work
+				setTimeout(() => {
+					if (!proc.killed) {
+						proc.kill("SIGKILL");
+					}
+				}, 5000);
+			}
+		};
+
+		// Handle abort signal
+		if (options?.signal) {
+			if (options.signal.aborted) {
+				killProcess();
+			} else {
+				options.signal.addEventListener("abort", killProcess, { once: true });
+			}
+		}
+
+		// Handle timeout
+		if (options?.timeout && options.timeout > 0) {
+			timeoutId = setTimeout(() => {
+				killProcess();
+			}, options.timeout);
+		}
 
 		proc.stdout?.on("data", (data) => {
 			stdout += data.toString();
@@ -45,11 +78,19 @@ async function exec(command: string, args: string[], cwd: string): Promise<ExecR
 		});
 
 		proc.on("close", (code) => {
-			resolve({ stdout, stderr, code: code ?? 0 });
+			if (timeoutId) clearTimeout(timeoutId);
+			if (options?.signal) {
+				options.signal.removeEventListener("abort", killProcess);
+			}
+			resolve({ stdout, stderr, code: code ?? 0, killed });
 		});
 
 		proc.on("error", (_err) => {
-			resolve({ stdout, stderr, code: 1 });
+			if (timeoutId) clearTimeout(timeoutId);
+			if (options?.signal) {
+				options.signal.removeEventListener("abort", killProcess);
+			}
+			resolve({ stdout, stderr, code: 1, killed });
 		});
 	});
 }
@@ -166,7 +207,7 @@ export class HookRunner {
 	 */
 	private createContext(): HookEventContext {
 		return {
-			exec: (command: string, args: string[]) => exec(command, args, this.cwd),
+			exec: (command: string, args: string[], options?: ExecOptions) => exec(command, args, this.cwd, options),
 			ui: this.uiContext,
 			hasUI: this.hasUI,
 			cwd: this.cwd,