refactor(coding-agent): replace AgentSessionRuntimeHost with closure-based AgentSessionRuntime

- Replace AgentSessionRuntimeHost and bootstrap abstractions with AgentSessionRuntime
- Runtime creation is now closure-based via CreateAgentSessionRuntimeFactory
- Factory closes over process-global fixed inputs, recreates cwd-bound services per effective cwd
- Session config (model, thinking, tools, scoped models) re-resolved per target cwd
- CLI resource paths resolved once at startup as absolute paths
- Swap lifecycle: teardown old, create next, apply next (hard fail on creation error)
- Unified diagnostics model (info/warning/error) for args, services, session resolution, resources
- No logging or process exits inside creation/parsing logic
- Removed session_directory support
- Removed session_switch and session_fork extension events (use session_start with reason)
- Moved package/config CLI to package-manager-cli.ts
- Fixed theme init for --resume session picker
- Fixed flaky reftable footer test (content-based polling)
- Fixed silent drop of unknown single-dash CLI flags
- Added error diagnostics for missing explicit CLI resource paths
- Updated SDK docs, examples, plans, exports, tests, changelog

fixes #2753

packages/coding-agent/docs/extensions.md

@@ -226,9 +226,8 @@ Run `npm install` in the extension directory, then imports from `node_modules/`
 ### Lifecycle Overview
 
 ```
-pi starts (CLI only)
+pi starts
   │
-  ├─► session_directory (CLI startup only, no ctx)
   ├─► session_start { reason: "startup" }
   └─► resources_discover { reason: "startup" }
       │
@@ -311,27 +310,6 @@ pi.on("resources_discover", async (event, _ctx) => {
 
 See [session.md](session.md) for session storage internals and the SessionManager API.
 
-#### session_directory
-
-Fired by the `pi` CLI during startup session resolution, before the initial session manager is created.
-
-This event is:
-- CLI-only. It is not emitted in SDK mode.
-- Startup-only. It is not emitted for later interactive `/new` or `/resume` actions.
-- Lower priority than `--session-dir` and `sessionDir` in `settings.json`.
-- Special-cased to receive no `ctx` argument.
-
-If multiple extensions return `sessionDir`, the last one wins.
-Combined precedence is: `--session-dir` CLI flag, then `sessionDir` in settings, then extension `session_directory` hooks.
-
-```typescript
-pi.on("session_directory", async (event) => {
-  return {
-    sessionDir: `/tmp/pi-sessions/${encodeURIComponent(event.cwd)}`,
-  };
-});
-```
-
 #### session_start
 
 Fired when a session is started, loaded, or reloaded.
@@ -759,9 +737,7 @@ Transforms chain across handlers. See [input-transform.ts](../examples/extension
 
 ## ExtensionContext
 
-All handlers except `session_directory` receive `ctx: ExtensionContext`.
-
-`session_directory` is a CLI startup hook and receives only the event.
+All handlers receive `ctx: ExtensionContext`.
 
 ### ctx.ui