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/examples/custom-tools/subagent/agents/scout.md

@@ -22,9 +22,6 @@ Strategy:
 
 Output format:
 
-## Query
-One line summary of what was searched.
-
 ## Files Retrieved
 List with exact line ranges:
 1. `path/to/file.ts` (lines 10-50) - Description of what's here