refactor: extract index construction state tracking into extension trait

Moves pipeline state bookkeeping, including sentinel file marking and spectrum persistence, into the algorithms' run and close methods. Introduces a crate-private extension trait to satisfy Rust's orphan rule while implementing construction-only operations on KmerIndex. Updates helper function visibility for cross-crate access and removes the now-empty index_layer module.

src/obikphylo/src/siblings/tests.rs

@@ -77,19 +77,14 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
         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.close().expect("close partition writers"); // also marks scatter done
     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 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");
-    idx.mark_counted().expect("mark_counted");
+    Counter::new(&idx).run(None::<fn(obisys::Progress)>).expect("count_kmer"); // also writes the spectrum + marks counted
     LayerBuilder::new(&idx)
         .run(None::<fn(obisys::Progress)>)
-        .expect("build_layers");
-    idx.mark_indexed().expect("mark_indexed");
+        .expect("build_layers"); // also marks indexed
     idx
 }