Rename Layer<D> to TypedLayer and introduce heterogeneous Layer enum

Renames `Layer<D>` to `TypedLayer<D>` to establish a distinct typed abstraction. Introduces a new heterogeneous `Layer` enum that unifies count and presence storage with runtime dispatch, delegating operations to the underlying typed variants. Updates cache, index, and phylo consumers to align with the renamed type and new extension traits, preserving full test suite stability while preparing the foundation for multi-partition caching.

src/obikindex/src/graph_pipeline.rs

@@ -10,7 +10,7 @@ use obipipeline::{
 
 use obidebruinj::GraphDeBruijn;
 use obikseq::CanonicalKmer;
-use obilayeredmap::{IndexMode, Layer};
+use obilayeredmap::{IndexMode, TypedLayer};
 use obiskio::{SKError, SKResult};
 
 use crate::common::olm_to_sk;
@@ -125,7 +125,7 @@ pub(crate) fn write_graph_as_unitigs(g: GraphDeBruijn, layer_dir: &Path) -> SKRe
     let n_kmers = g.len();
     g.compute_degrees_and_mark_starts();
     std::fs::create_dir_all(layer_dir)?;
-    let mut uw = Layer::<()>::unitig_writer(layer_dir).map_err(|e| olm_to_sk(e, "graph pipeline"))?;
+    let mut uw = TypedLayer::<()>::unitig_writer(layer_dir).map_err(|e| olm_to_sk(e, "graph pipeline"))?;
     g.try_for_each_unitig(|unitig| uw.write(unitig))?;
     uw.close()?;
     drop(g);
@@ -134,7 +134,7 @@ pub(crate) fn write_graph_as_unitigs(g: GraphDeBruijn, layer_dir: &Path) -> SKRe
 
 // ── materialize_layer ─────────────────────────────────────────────────────────
 
-/// Phase 2 (full): write_graph_as_unitigs + `Layer::<()>::build`.
+/// Phase 2 (full): write_graph_as_unitigs + `TypedLayer::<()>::build`.
 ///
 /// Returns n_kmers.
 pub(crate) fn materialize_layer(
@@ -145,7 +145,7 @@ pub(crate) fn materialize_layer(
 ) -> SKResult<usize> {
     let n = write_graph_as_unitigs(g, layer_dir)?;
     debug!("materialize_layer: unitigs written ({n} kmers), building MPHF");
-    Layer::<()>::build(layer_dir, block_bits, evidence)
+    TypedLayer::<()>::build(layer_dir, block_bits, evidence)
         .map_err(|e| olm_to_sk(e, "graph pipeline"))?;
     debug!("materialize_layer: MPHF build done");
     Ok(n)

src/obikindex/src/index_layer.rs

@@ -6,7 +6,7 @@ use epserde::prelude::*;
 use obicompactvec::{PersistentCompactIntMatrix, PersistentCompactIntVec};
 use obidebruinj::GraphDeBruijn;
 use obilayeredmap::meta::PartitionMeta;
-use obilayeredmap::{IndexMode, layer::Layer};
+use obilayeredmap::{IndexMode, layer::TypedLayer};
 use obiskio::{SKError, SKFileMeta, SKFileReader};
 use ptr_hash::{PtrHash, bucket_fn::CubicEps, hash::Xx64};
 
@@ -96,7 +96,7 @@ impl KmerIndex {
         let n_kmers =
             if with_counts {
                 let n = write_graph_as_unitigs(g, &layer_dir)?;
-                Layer::<PersistentCompactIntMatrix>::build(&layer_dir, block_bits, mode, |kmer| {
+                TypedLayer::<PersistentCompactIntMatrix>::build(&layer_dir, block_bits, mode, |kmer| {
                     match (&mphf1_opt, &counts1_opt) {
                         (Some(mphf), Some(counts)) => counts.get(mphf.index(&kmer.raw())),
                         _ => 1,

src/obikindex/src/merge_layer/mod.rs

@@ -20,7 +20,7 @@ use tracing::debug;
 
 use obicompactvec::{PersistentBitMatrixBuilder, PersistentCompactIntMatrixBuilder};
 use obikseq::CanonicalKmer;
-use obilayeredmap::{IndexMode, Layer, LayeredMap, MphfOnly, layer_dir};
+use obilayeredmap::{IndexMode, TypedLayer, LayeredMap, MphfOnly, layer_dir};
 use obiskio::{SKError, SKResult, UnitigFileReader};
 
 use crate::common::{ColBuilder, load_meta, olm_to_sk};
@@ -232,7 +232,7 @@ impl KmerIndex {
         // (all slots true — every kmer in those layers belongs to genome_0).
         if n_dst_genomes == 1 && mode == MergeMode::Presence {
             for l in 0..n_dst_layers {
-                Layer::<()>::init_presence_matrix(
+                TypedLayer::<()>::init_presence_matrix(
                     &layer_dir(&dst_index_dir, l),
                     dst_map.layer(l).n(),
                 )

src/obikindex/src/reindex.rs

@@ -1,4 +1,4 @@
-use obilayeredmap::{IndexMode, layer::Layer};
+use obilayeredmap::{IndexMode, layer::TypedLayer};
 use obisys::{Reporter, Stage, progress_bar};
 use std::fs;
 use std::path::Path;
@@ -90,10 +90,10 @@ fn reindex_partition(
 fn reindex_layer(layer_dir: &Path, target: &IndexMode, block_bits: u8) -> OKIResult<()> {
     match target {
         IndexMode::Exact => {
-            Layer::<()>::build_exact_evidence(layer_dir, block_bits).map_err(olm_to_oki)?;
+            TypedLayer::<()>::build_exact_evidence(layer_dir, block_bits).map_err(olm_to_oki)?;
         }
         IndexMode::Approx { b, z } | IndexMode::Hybrid { b, z } => {
-            Layer::<()>::build_approx_evidence(layer_dir, *b, *z).map_err(olm_to_oki)?;
+            TypedLayer::<()>::build_approx_evidence(layer_dir, *b, *z).map_err(olm_to_oki)?;
         }
     }
     remove_stale_evidence(layer_dir, target)