Add project-specific settings and SettingsManager factories

- SettingsManager now loads .pi/settings.json from cwd (project settings)
- Project settings merge with global settings (deep merge for objects)
- Setters only modify global settings, project settings are read-only
- Add static factories: SettingsManager.create(cwd?, agentDir?), SettingsManager.inMemory(settings?)
- Add applyOverrides() for programmatic overrides
- Replace 'settings' option with 'settingsManager' in CreateAgentSessionOptions
- Update examples to use new pattern

Incorporates PR #276 approach

packages/coding-agent/src/utils/shell.ts

@@ -34,7 +34,7 @@ export function getShellConfig(): { shell: string; args: string[] } {
 		return cachedShellConfig;
 	}
 
-	const settings = new SettingsManager();
+	const settings = SettingsManager.create();
 	const customShellPath = settings.getShellPath();
 
 	// 1. Check user-specified shell path