feat(coding-agent): package deduplication and collision detection

- Package deduplication: same package in global+project, project wins
- Collision detection for skills, prompts, and themes with ResourceCollision type
- PathMetadata tracking with parent directory lookup for file paths
- Display improvements: section headers, sorted groups, accent colors for packages
- pi list shows full paths below package names
- Extension loader discovers files in directories without index.ts
- In-memory SettingsManager properly tracks project settings

fixes #645

packages/coding-agent/src/index.ts

@@ -118,9 +118,15 @@ export {
 export type { ReadonlyFooterDataProvider } from "./core/footer-data-provider.js";
 export { convertToLlm } from "./core/messages.js";
 export { ModelRegistry } from "./core/model-registry.js";
-export type { PackageManager, ProgressCallback, ProgressEvent } from "./core/package-manager.js";
+export type {
+	PackageManager,
+	PathMetadata,
+	ProgressCallback,
+	ProgressEvent,
+	ResolvedPaths,
+} from "./core/package-manager.js";
 export { DefaultPackageManager } from "./core/package-manager.js";
-export type { ResourceDiagnostic, ResourceLoader } from "./core/resource-loader.js";
+export type { ResourceCollision, ResourceDiagnostic, ResourceLoader } from "./core/resource-loader.js";
 export { DefaultResourceLoader } from "./core/resource-loader.js";
 // SDK for programmatic usage
 export {