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/src/modes/rpc/rpc-mode.ts

@@ -12,7 +12,7 @@
  */
 
 import * as crypto from "node:crypto";
-import type { AgentSessionRuntimeHost } from "../../core/agent-session-runtime.js";
+import type { AgentSessionRuntime } from "../../core/agent-session-runtime.js";
 import type {
 	ExtensionUIContext,
 	ExtensionUIDialogOptions,
@@ -43,7 +43,7 @@ export type {
  * Run in RPC mode.
  * Listens for JSON commands on stdin, outputs events and responses on stdout.
  */
-export async function runRpcMode(runtimeHost: AgentSessionRuntimeHost): Promise<never> {
+export async function runRpcMode(runtimeHost: AgentSessionRuntime): Promise<never> {
 	takeOverStdout();
 	let session = runtimeHost.session;
 	let unsubscribe: (() => void) | undefined;
@@ -628,29 +628,49 @@ export async function runRpcMode(runtimeHost: AgentSessionRuntimeHost): Promise<
 	}
 
 	const handleInputLine = async (line: string) => {
+		let parsed: unknown;
 		try {
-			const parsed = JSON.parse(line);
+			parsed = JSON.parse(line);
+		} catch (parseError: unknown) {
+			output(
+				error(
+					undefined,
+					"parse",
+					`Failed to parse command: ${parseError instanceof Error ? parseError.message : String(parseError)}`,
+				),
+			);
+			return;
+		}
 
-			// Handle extension UI responses
-			if (parsed.type === "extension_ui_response") {
-				const response = parsed as RpcExtensionUIResponse;
-				const pending = pendingExtensionRequests.get(response.id);
-				if (pending) {
-					pendingExtensionRequests.delete(response.id);
-					pending.resolve(response);
-				}
-				return;
+		// Handle extension UI responses
+		if (
+			typeof parsed === "object" &&
+			parsed !== null &&
+			"type" in parsed &&
+			parsed.type === "extension_ui_response"
+		) {
+			const response = parsed as RpcExtensionUIResponse;
+			const pending = pendingExtensionRequests.get(response.id);
+			if (pending) {
+				pendingExtensionRequests.delete(response.id);
+				pending.resolve(response);
 			}
+			return;
+		}
 
-			// Handle regular commands
-			const command = parsed as RpcCommand;
+		const command = parsed as RpcCommand;
+		try {
 			const response = await handleCommand(command);
 			output(response);
-
-			// Check for deferred shutdown request (idle between commands)
 			await checkShutdownRequested();
-		} catch (e: any) {
-			output(error(undefined, "parse", `Failed to parse command: ${e.message}`));
+		} catch (commandError: unknown) {
+			output(
+				error(
+					command.id,
+					command.type,
+					commandError instanceof Error ? commandError.message : String(commandError),
+				),
+			);
 		}
 	};