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/compaction-extensions.test.ts

@@ -21,7 +21,7 @@ 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 { createSyntheticSourceInfo } from "../src/core/source-info.js";
-import { codingTools } from "../src/core/tools/index.js";
+import { createCodingTools } from "../src/index.js";
 import { createTestResourceLoader } from "./utilities.js";
 
 const API_KEY = process.env.ANTHROPIC_OAUTH_TOKEN || process.env.ANTHROPIC_API_KEY;
@@ -92,7 +92,7 @@ describe.skipIf(!API_KEY)("Compaction extensions", () => {
 			initialState: {
 				model,
 				systemPrompt: "You are a helpful assistant. Be concise.",
-				tools: codingTools,
+				tools: createCodingTools(process.cwd()),
 			},
 		});