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/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 },