Refactor kmer index package to use disk-based partitioning with minimizer
- Replace roaring64 bitmaps with disk-based kmer index
- Implement partitioned kmer sets with delta-varint encoding
- Add support for frequency filtering during construction
- Introduce new builder pattern for index construction
- Add streaming operations for set operations (union, intersect, etc.)
- Add support for super-kmer encoding during construction
- Update command line tool to use new index format
- Remove dependency on roaring bitmap library
This change introduces a new architecture for kmer indexing that is more memory efficient and scalable for large datasets.
