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/README.md

@@ -595,10 +595,12 @@ export default function (pi: HookAPI) {
 
 Custom tools let you extend the built-in toolset (read, write, edit, bash, ...) and are called by the LLM directly. They are TypeScript modules that define tools with optional custom TUI integration for getting user input and custom tool call and result rendering.
 
-**Tool locations:**
-- Global: `~/.pi/agent/tools/*.ts`
-- Project: `.pi/tools/*.ts`
-- CLI: `--tool <path>`
+**Tool locations (auto-discovered):**
+- Global: `~/.pi/agent/tools/*/index.ts`
+- Project: `.pi/tools/*/index.ts`
+
+**Explicit paths:**
+- CLI: `--tool <path>` (any .ts file)
 - Settings: `customTools` array in `settings.json`
 
 **Quick example:**