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/modes/print-mode.ts

@@ -109,4 +109,13 @@ export async function runPrintMode(
 			}
 		}
 	}
+
+	// Ensure stdout is fully flushed before returning
+	// This prevents race conditions where the process exits before all output is written
+	await new Promise<void>((resolve, reject) => {
+		process.stdout.write("", (err) => {
+			if (err) reject(err);
+			else resolve();
+		});
+	});
 }