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/CHANGELOG.md

@@ -6,8 +6,16 @@
 
 - **Subagent orchestration example**: Added comprehensive custom tool example for spawning and orchestrating sub-agents with isolated context windows. Includes scout/planner/reviewer/worker agents and workflow commands for multi-agent pipelines. ([#215](https://github.com/badlogic/pi-mono/pull/215) by [@nicobailon](https://github.com/nicobailon))
 
+- **`pi.exec()` signal and timeout support**: Custom tools and hooks can now pass `{ signal, timeout }` options to `pi.exec()` for cancellation and timeout handling. The result includes a `killed` flag when the process was terminated.
+
+### Fixed
+
+- **JSON mode stdout flush**: Fixed race condition where `pi --mode json` could exit before all output was written to stdout, causing consumers to miss final events.
+
 ### Breaking Changes
 
+- **Custom tools now require `index.ts` entry point**: Auto-discovered custom tools must be in a subdirectory with an `index.ts` file. The old pattern `~/.pi/agent/tools/mytool.ts` must become `~/.pi/agent/tools/mytool/index.ts`. This allows multi-file tools to import helper modules. Explicit paths via `--tool` or `settings.json` still work with any `.ts` file.
+
 - **Hook `tool_result` event restructured**: The `ToolResultEvent` now exposes full tool result data instead of just text. ([#233](https://github.com/badlogic/pi-mono/pull/233))
   - Removed: `result: string` field
   - Added: `content: (TextContent | ImageContent)[]` - full content array