This commit renames the `Layer` type to `KmerLayer` throughout the `obikindex` and `obikphylo` crates. All imports, struct fields, function signatures, pattern matches, and instantiation calls have been updated accordingly. The change is a purely structural refactor that tightens type constraints without altering runtime behavior or data models.
Introduce a dedicated LayerBuilder struct to orchestrate parallel layer 0 construction across partitions. The fluent API supports configurable abundance thresholds and intermediate artifact retention. Parallel execution is delegated to a NUMA-aware PartitionRunner scheduler, while progress reporting and stage timing are shifted to the command layer. A new mark_indexed method cleanly separates state tracking from orchestration by generating a completion sentinel.
Decouple k-mer counting from the partitioner by introducing a new `Counter` struct. The module exposes a fluent builder API with optional partial file retention, executes partition processing in parallel via Rayon with memory-aware chunk sizing, and integrates thread-safe progress callbacks. Update all callers to use the new counter, simplify test pipelines by removing serialization overhead, and clarify algorithm separation in module documentation.
Eric Coissac