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/examples/sdk/06-extensions.ts

@@ -13,12 +13,14 @@
  *   export default function (pi: ExtensionAPI) { ... }
  */
 
-import { createAgentSession, DefaultResourceLoader, SessionManager } from "@mariozechner/pi-coding-agent";
+import { createAgentSession, DefaultResourceLoader, getAgentDir, SessionManager } from "@mariozechner/pi-coding-agent";
 
 // Extensions are discovered automatically from standard locations.
 // You can also add paths via settings.json or DefaultResourceLoader options.
 
 const resourceLoader = new DefaultResourceLoader({
+	cwd: process.cwd(),
+	agentDir: getAgentDir(),
 	additionalExtensionPaths: ["./my-logging-extension.ts", "./my-safety-extension.ts"],
 	extensionFactories: [
 		(pi) => {