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/04-skills.ts

@@ -9,6 +9,7 @@ import {
 	createAgentSession,
 	createSyntheticSourceInfo,
 	DefaultResourceLoader,
+	getAgentDir,
 	SessionManager,
 	type Skill,
 } from "@mariozechner/pi-coding-agent";
@@ -24,6 +25,8 @@ const customSkill: Skill = {
 };
 
 const loader = new DefaultResourceLoader({
+	cwd: process.cwd(),
+	agentDir: getAgentDir(),
 	skillsOverride: (current) => {
 		const filteredSkills = current.skills.filter((s) => s.name.includes("browser") || s.name.includes("search"));
 		return {