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/mom/src/agent.ts

@@ -458,6 +458,7 @@ function createRunner(sandboxConfig: SandboxConfig, channelId: string, channelDi
 		getAgentsFiles: () => ({ agentsFiles: [] }),
 		getSystemPrompt: () => systemPrompt,
 		getAppendSystemPrompt: () => [],
+		getPathMetadata: () => new Map(),
 		reload: async () => {},
 	};