Refactor indexing pipeline and partition path resolution

Invert dependencies by moving partition path primitives to a dedicated module and updating the index crate accordingly. Reshape the partition router to accept a mutable index reference, enabling chainable configuration and resolving lifetime issues with explicit drops. Shift orchestration logic from the index crate to the CLI, replacing monolithic scatter calls with discrete dereplication and counting steps. Introduce a generic progress callback API to decouple rate calculation from UI rendering, and correct file I/O paths to route layer-0 artifacts under the partition index directory.

src/obikphylo/src/siblings/tests.rs

@@ -7,6 +7,7 @@ use obisys::Reporter;
 use tempfile::tempdir;
 
 use obikindex::{GenomeInfo, IndexConfig, KmerIndex, MergeMode};
+use obikpartitionner::PartitionRouter;
 
 use super::alignment::SnpAlignmentExt;
 use super::build::SiblingAnnexBuildExt;
@@ -64,19 +65,24 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
         evidence: obilayeredmap::IndexMode::Exact,
         block_bits: 0,
     };
-    let mut idx = KmerIndex::create(&index_path, config, Some(GenomeInfo::new(label)), false)
+    let mut idx = KmerIndex::create(&index_path, config, Some(GenomeInfo::new(label)))
         .expect("create");
 
     let mut rep = Reporter::new();
     let stream = obiread::open_nuc_stream(fasta_path.to_str().unwrap(), K).expect("open fasta");
-    let mut router = idx.partition_router().expect("partition_router");
+    let mut router = PartitionRouter::new(&mut idx);
     for page in stream {
         let batch = obiskbuilder::build_superkmers_page(page, K, /* level_max */ 1, /* theta */ 0.0);
         router.write_batch(batch).expect("write_batch");
     }
     router.close().expect("close partition writers");
+    router.dereplicate().expect("dereplicate");
+    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
+
     idx.mark_scattered().expect("mark_scattered");
-    idx.dereplicate_and_count(false, &mut rep).expect("dereplicate_and_count");
+    idx.write_spectrum(spectrum.f0, spectrum.f1, &spectrum.counts).expect("write_spectrum");
+    idx.mark_counted().expect("mark_counted");
     idx.build_layers(1, None, false, &mut rep).expect("build_layers");
     idx
 }