Extract dereplication logic into obikderep crate and centralize paths

Move partition dereplication logic into a dedicated `obikderep` crate that implements a two-phase hash-split/merge strategy with Rayon for parallel processing. Centralize superkmer file path construction in `obilayeredmap` and update dependent crates to use the new pipeline and shared path helpers. Adjust test suites to explicitly invoke the dereplication step.

src/obikphylo/Cargo.toml

@@ -20,6 +20,7 @@ rayon            = "1"
 tracing          = "0.1.44"
 
 [dev-dependencies]
-obiread  = { path = "../obiread" }
+obiread   = { path = "../obiread" }
+obikderep = { path = "../obikderep" }
 tempfile = "3"
 tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }

src/obikphylo/src/siblings/tests.rs

@@ -6,6 +6,7 @@ use obilayeredmap::MphfLayer;
 use obisys::Reporter;
 use tempfile::tempdir;
 
+use obikderep::Dereplicator;
 use obikindex::{GenomeInfo, IndexConfig, KmerIndex, MergeMode};
 use obikpartitionner::PartitionRouter;
 
@@ -76,7 +77,10 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
         router.write_batch(batch).expect("write_batch");
     }
     router.close().expect("close partition writers");
-    router.dereplicate().expect("dereplicate");
+    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