feat(core-pipeline): implement the HARP core pipeline

[AntonCoon]

This PR introduces the foundational architecture for HARP's haplotype allele counting pipeline.

Current progress includes:

• Custom data types: VariantKey, Counts, Variant
• I/O function to load bi-allelic SNVs from VCF files
• Unit tests covering types and I/O

Subsequent commits in this branch will implement:

• Chunk-based processing of BAM/VCF regions
• Parallel execution
• Full end-to-end aggregation and TSV output

This structure ensures each commit is atomic, testable, and passes CI, while the PR represents the full pipeline feature.