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/main.ts

@@ -288,7 +288,7 @@ export async function main(args: string[]) {
 	const isInteractive = !parsed.print && parsed.mode === undefined;
 	const mode = parsed.mode || "text";
 
-	const settingsManager = new SettingsManager();
+	const settingsManager = SettingsManager.create(cwd);
 	initTheme(settingsManager.getTheme(), isInteractive);
 
 	let scopedModels: ScopedModel[] = [];