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/examples/sdk/12-full-control.ts

@@ -53,6 +53,7 @@ const resourceLoader: ResourceLoader = {
 	getSystemPrompt: () => `You are a minimal assistant.
 Available: read, bash. Be concise.`,
 	getAppendSystemPrompt: () => [],
+	getPathMetadata: () => new Map(),
 	reload: async () => {},
 };