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",