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/agent-session-compaction.test.ts

@@ -18,7 +18,7 @@ import { AuthStorage } from "../src/core/auth-storage.js";
 import { ModelRegistry } from "../src/core/model-registry.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";
 import { API_KEY, createTestResourceLoader } from "./utilities.js";
 
 describe.skipIf(!API_KEY)("AgentSession compaction e2e", () => {
@@ -52,7 +52,7 @@ describe.skipIf(!API_KEY)("AgentSession compaction e2e", () => {
 			initialState: {
 				model,
 				systemPrompt: "You are a helpful assistant. Be concise.",
-				tools: codingTools,
+				tools: createCodingTools(process.cwd()),
 			},
 		});