Extract k-mer counting logic into a dedicated counter module

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.

src/obikphylo/src/siblings/tests.rs

@@ -6,6 +6,7 @@ use obikindex::layer::MphfLayer;
 use obisys::Reporter;
 use tempfile::tempdir;
 
+use obikindexer::algorithms::counter::Counter;
 use obikindexer::algorithms::dereplicator::Dereplicator;
 use obikindexer::algorithms::partitionner::PartitionRouter;
 use obikindex::{GenomeInfo, IndexConfig, KmerIndex, MergeMode};
@@ -80,9 +81,7 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
     drop(router); // ends the borrow of `idx` early — `PartitionRouter`'s `Drop` impl would otherwise extend it to the end of scope
 
     Dereplicator::new(&idx).run(None::<fn(obisys::Progress)>).expect("dereplicate");
-    let router = PartitionRouter::new(&mut idx);
-    let spectrum = router.count_kmer(false).expect("count_kmer");
-    drop(router); // ends the borrow of `idx` early — `PartitionRouter`'s `Drop` impl would otherwise extend it to the end of scope
+    let spectrum = Counter::new(&idx).run(None::<fn(obisys::Progress)>).expect("count_kmer");
 
     idx.mark_scattered().expect("mark_scattered");
     idx.write_spectrum(spectrum.f0, spectrum.f1, &spectrum.counts).expect("write_spectrum");