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/pods/package.json

@@ -4,7 +4,7 @@
 	"description": "CLI tool for managing vLLM deployments on GPU pods",
 	"type": "module",
 	"bin": {
-		"pi": "dist/cli.js"
+		"pi-pods": "dist/cli.js"
 	},
 	"scripts": {
 		"clean": "rm -rf dist",