refactor: Complete Repository.cs extraction into partial classes

Successfully split the 2549-line Repository.cs into focused partial classes:
- Repository.State.cs (120 lines): Shared state and thread-safe helpers
- Repository.Refresh.cs (618 lines): All refresh operations
- Repository.GitOperations.cs (434 lines): Git command operations
- Repository.Search.cs (438 lines): Search and filter functionality
- Repository.cs (1384 lines): Core functionality and UI management

Key improvements:
- 46% reduction in main file size for better maintainability
- Logical grouping by functional areas
- Thread-safe UI dispatch patterns throughout
- Preserved all existing functionality
- No breaking changes to public API
- Optimized with parallel operations and caching

The refactoring follows .NET 9 best practices with protected internal
fields for cross-partial access and maintains MVVM architecture.

Author: biancode