Formalize the two-phase MPHF indexing architecture and update Phase 6 to use `evidence.bin` for direct kmer extraction. Simplify the evidence and unitig storage layouts to flat packed formats enabling O(1) random access. Introduce aggregation traits (`ColumnWeights`, `CountPartials`, `BitPartials`) to support additive distance metric decomposition across partitions. Narrow the documented scope from metagenomic to individual genome datasets, and replace speculative open questions with concrete implementation specifications.
Introduce the `obilayeredmap` specification and persistent MPHF-based index architecture for incremental multi-dataset indexing. Implement chunked binary serialization with a fixed `u8` k-mer count limit (256) and overlapping super-kmer segments. Add memory-mapped I/O and a companion `.idx` index file for allocation-free, O(1) unitig access. Update MkDocs navigation, enhance the k-mer comparison script, and add comprehensive tests for serialization, partitioning, and file I/O pipelines.
Eric Coissac