feat(mcp-server): update to use centralized storage

Update MCP server to use centralized storage paths for repository
indexes and GitHub state.

Implementation:
- Updated dev-agent-mcp.ts to use getStoragePath() and getStorageFilePaths()
- MCP server now uses centralized ~/.dev-agent/indexes/{repo-hash}/ structure
- Added infrastructure for lazy loading (prefixed with _ for future use)
- Updated RepositoryIndexer and GitHubIndexer to use centralized paths

Features:
- Centralized storage for all indexed repositories
- Lazy loading infrastructure (foundation for future optimization)
- Consistent storage paths across CLI and MCP server

Testing:
- MCP server updated and verified
- Storage path resolution working correctly

Issue: #52

Author: prosdev