refactor: merge KmerPartitions into KmerIndex and rename obikpartition

Consolidates partition logic, metadata storage, and layer management directly into KmerIndex. Renames obikpartitionner to obikpartition, retaining only PartitionRouter for superkmer routing. Removes intermediate .partition() accessors in favor of direct methods on the index and updates PartitionCache::build to accept &KmerIndex directly. Derives n_partitions from config.n_bits and consolidates k-mer/minimizer sizes into IndexMeta.config. Fixes a regression where PartitionRouter::open incorrectly defaulted to closed.

src/obikphylo/src/siblings/build.rs

@@ -4,7 +4,6 @@ use std::sync::atomic::Ordering;
 
 use rayon::prelude::*;
 
-use obikpartitionner::KmerPartitions;
 use obikseq::CanonicalKmer;
 use obilayeredmap::MphfLayer;
 use obilayeredmap::meta::IndexMode;
@@ -12,7 +11,7 @@ use obipipeline::ThrottleGuard;
 use obisys::progress_bar;
 
 use obikindex::KmerIndex;
-use obikindex::{OKIError, OKIResult};
+use obikindex::OKIResult;
 
 use super::cache::PartitionCache;
 use super::helpers::{central_base, is_minorant};
@@ -76,19 +75,10 @@ pub trait SiblingAnnexBuildExt {
 impl SiblingAnnexBuildExt for KmerIndex {
     fn build_sibling_annex(&self) -> OKIResult<()> {
         let n_parts = self.n_partitions();
-        let n_bits = n_parts.trailing_zeros() as usize;
-
-        let partition = KmerPartitions::open_with_config(
-            self.root_path(),
-            self.kmer_size(),
-            self.minimizer_size(),
-            n_bits,
-        )
-        .map_err(OKIError::Partition)?;
 
         tracing::info!("opening {n_parts} partition(s) for the sibling-annex sweep");
         let cache = Arc::new(PartitionCache::build(
-            &partition,
+            self,
             n_parts,
             self.meta().config.with_counts,
         )?);
@@ -96,18 +86,18 @@ impl SiblingAnnexBuildExt for KmerIndex {
         let pb = progress_bar("sibling_annex", n_parts as u64, "partitions");
         let mut total_slots: u64 = 0;
         for part in 0..n_parts {
-            let index_dir = self.partition().index_dir(part);
+            let index_dir = self.index_dir(part);
             if !index_dir.exists() {
                 pb.inc(1);
                 continue;
             }
-            let meta = self.partition().partition_meta(part)?;
+            let meta = self.partition_meta(part)?;
 
             let mut part_slots: u64 = 0;
             for l in 0..meta.n_layers {
                 part_slots += build_layer_sibling_annex(
                     self,
-                    &self.partition().layer_dir(part, l),
+                    &self.layer_dir(part, l),
                     &meta.mode,
                     n_parts,
                     l,