fix(coding-agent): remove process-cwd tool singletons and use tool-name allowlists

- switch SDK/CLI tool selection to name-based allowlists
- apply allowlists across built-in, extension, and SDK tools
- remove ambient process.cwd defaults from core tooling and resource helpers
- update tests, examples, and TUI callers for explicit cwd plumbing
- add regression coverage for extension tool filtering

closes #3452
closes #2835

packages/coding-agent/test/utilities.ts

@@ -17,7 +17,7 @@ import { ModelRegistry } from "../src/core/model-registry.js";
 import type { ResourceLoader } from "../src/core/resource-loader.js";
 import { SessionManager } from "../src/core/session-manager.js";
 import { SettingsManager } from "../src/core/settings-manager.js";
-import { codingTools } from "../src/core/tools/index.js";
+import { createCodingTools } from "../src/index.js";
 
 /**
  * API key for authenticated tests. Tests using this should be wrapped in
@@ -242,7 +242,7 @@ export function createTestSession(options: TestSessionOptions = {}): TestSession
 		initialState: {
 			model,
 			systemPrompt: options.systemPrompt ?? "You are a helpful assistant. Be extremely concise.",
-			tools: codingTools,
+			tools: createCodingTools(process.cwd()),
 		},
 	});