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/src/utils/shell.ts

@@ -53,7 +53,7 @@ export function getShellConfig(): { shell: string; args: string[] } {
 		return cachedShellConfig;
 	}
 
-	const settings = SettingsManager.create();
+	const settings = SettingsManager.create(process.cwd());
 	const customShellPath = settings.getShellPath();
 
 	// 1. Check user-specified shell path