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/main.ts

@@ -445,6 +445,10 @@ export async function main(args: string[]) {
 		await runPrintMode(session, mode, parsed.messages, initialMessage, initialAttachments);
 		// Clean up and exit (file watchers keep process alive)
 		stopThemeWatcher();
+		// Wait for stdout to fully flush before exiting
+		if (process.stdout.writableLength > 0) {
+			await new Promise<void>((resolve) => process.stdout.once("drain", resolve));
+		}
 		process.exit(0);
 	}
 }