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/args.test.ts

@@ -270,9 +270,20 @@ describe("parseArgs", () => {
 			expect(result.messages).toEqual(["explain this"]);
 		});
 
-		test("ignores unknown flags starting with -", () => {
+		test("captures unknown long flags with string values", () => {
 			const result = parseArgs(["--unknown-flag", "message"]);
-			expect(result.messages).toEqual(["message"]);
+			expect(result.messages).toEqual([]);
+			expect(result.unknownFlags.get("unknown-flag")).toBe("message");
+		});
+
+		test("captures unknown boolean long flags", () => {
+			const result = parseArgs(["--unknown-flag"]);
+			expect(result.unknownFlags.get("unknown-flag")).toBe(true);
+		});
+
+		test("captures unknown long flags with equals syntax", () => {
+			const result = parseArgs(["--unknown-flag=value"]);
+			expect(result.unknownFlags.get("unknown-flag")).toBe("value");
 		});
 	});