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/03-custom-prompt.ts

@@ -4,10 +4,15 @@
  * Shows how to replace or modify the default system prompt.
  */
 
-import { createAgentSession, DefaultResourceLoader, SessionManager } from "@mariozechner/pi-coding-agent";
+import { createAgentSession, DefaultResourceLoader, getAgentDir, SessionManager } from "@mariozechner/pi-coding-agent";
+
+const cwd = process.cwd();
+const agentDir = getAgentDir();
 
 // Option 1: Replace prompt entirely
 const loader1 = new DefaultResourceLoader({
+	cwd,
+	agentDir,
 	systemPromptOverride: () => `You are a helpful assistant that speaks like a pirate.
 Always end responses with "Arrr!"`,
 	// Needed to avoid DefaultResourceLoader appending APPEND_SYSTEM.md from ~/.pi/agent or <cwd>/.pi.
@@ -32,6 +37,8 @@ console.log("\n");
 
 // Option 2: Append instructions to the default prompt
 const loader2 = new DefaultResourceLoader({
+	cwd,
+	agentDir,
 	appendSystemPromptOverride: (base) => [
 		...base,
 		"## Additional Instructions\n- Always be concise\n- Use bullet points when listing things",

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 {

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) => {

packages/coding-agent/examples/sdk/07-context-files.ts

@@ -4,10 +4,12 @@
  * Context files provide project-specific instructions loaded into the system prompt.
  */
 
-import { createAgentSession, DefaultResourceLoader, SessionManager } from "@mariozechner/pi-coding-agent";
+import { createAgentSession, DefaultResourceLoader, getAgentDir, SessionManager } from "@mariozechner/pi-coding-agent";
 
 // Disable context files entirely by returning an empty list in agentsFilesOverride.
 const loader = new DefaultResourceLoader({
+	cwd: process.cwd(),
+	agentDir: getAgentDir(),
 	agentsFilesOverride: (current) => ({
 		agentsFiles: [
 			...current.agentsFiles,

packages/coding-agent/examples/sdk/08-prompt-templates.ts

@@ -8,6 +8,7 @@ import {
 	createAgentSession,
 	createSyntheticSourceInfo,
 	DefaultResourceLoader,
+	getAgentDir,
 	type PromptTemplate,
 	SessionManager,
 } from "@mariozechner/pi-coding-agent";
@@ -26,6 +27,8 @@ const deployTemplate: PromptTemplate = {
 };
 
 const loader = new DefaultResourceLoader({
+	cwd: process.cwd(),
+	agentDir: getAgentDir(),
 	promptsOverride: (current) => ({
 		prompts: [...current.prompts, deployTemplate],
 		diagnostics: current.diagnostics,

packages/coding-agent/examples/sdk/10-settings.ts

@@ -6,12 +6,14 @@
 
 import { createAgentSession, SessionManager, SettingsManager } from "@mariozechner/pi-coding-agent";
 
+const cwd = process.cwd();
+
 // Load current settings (merged global + project)
-const settingsManagerFromDisk = SettingsManager.create();
+const settingsManagerFromDisk = SettingsManager.create(cwd);
 console.log("Current settings:", JSON.stringify(settingsManagerFromDisk.getGlobalSettings(), null, 2));
 
 // Override specific settings
-const settingsManager = SettingsManager.create();
+const settingsManager = SettingsManager.create(cwd);
 settingsManager.applyOverrides({
 	compaction: { enabled: false },
 	retry: { enabled: true, maxRetries: 5, baseDelayMs: 1000 },