refactor: streamline merge pipeline and MPHF indexing

Replace mphf.find() with direct mphf.index() calls to eliminate absence checks and fallback vectors. Introduce a lightweight MphfOnly wrapper for faster index loading, and standardize k-mer iteration across merge and rebuild layers. Update IndexMeta configuration and n_new calculation to leverage MPHF cardinality, streamlining the overall merge pipeline.

src/obikindex/src/merge.rs

@@ -96,7 +96,7 @@ impl KmerIndex {
         let mut meta = IndexMeta::read(output).map_err(OKIError::Io)?;
         meta.genomes = all_genomes;
         meta.config.with_counts = mode == MergeMode::Count;
-        meta.config.evidence = evidence;
+        meta.config.evidence = evidence.clone();
         meta.write(output)?;
 
         // In presence/absence mode, purge counts/ directories inherited from
@@ -147,7 +147,7 @@ impl KmerIndex {
                 .filter_map(|i| {
                     let srcs: Vec<(&obikpartitionner::KmerPartition, usize)> =
                         remaining_sources.iter().map(|s| (&s.partition, s.meta.genomes.len())).collect();
-                    let result = dst_partition.merge_partition(i, &srcs, mode, n_dst_genomes, block_bits).err();
+                    let result = dst_partition.merge_partition(i, &srcs, mode, n_dst_genomes, block_bits, &evidence).err();
                     pb.inc(1);
                     result
                 })