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/test/settings-manager.test.ts

@@ -155,7 +155,7 @@ describe("SettingsManager", () => {
 	});
 
 	describe("reload", () => {
-		it("should reload global settings from disk", () => {
+		it("should reload global settings from disk", async () => {
 			const settingsPath = join(agentDir, "settings.json");
 			writeFileSync(
 				settingsPath,
@@ -176,21 +176,21 @@ describe("SettingsManager", () => {
 				}),
 			);
 
-			manager.reload();
+			await manager.reload();
 
 			expect(manager.getTheme()).toBe("light");
 			expect(manager.getExtensionPaths()).toEqual(["/after.ts"]);
 			expect(manager.getDefaultModel()).toBe("claude-sonnet");
 		});
 
-		it("should keep previous settings when file is invalid", () => {
+		it("should keep previous settings when file is invalid", async () => {
 			const settingsPath = join(agentDir, "settings.json");
 			writeFileSync(settingsPath, JSON.stringify({ theme: "dark" }));
 
 			const manager = SettingsManager.create(projectDir, agentDir);
 
 			writeFileSync(settingsPath, "{ invalid json");
-			manager.reload();
+			await manager.reload();
 
 			expect(manager.getTheme()).toBe("dark");
 		});