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/Cargo.lock

@@ -1595,18 +1595,26 @@ name = "obikindex"
 version = "0.1.0"
 dependencies = [
  "anyhow",
+ "cacheline-ef",
  "crossbeam-channel",
+ "epserde",
  "hwlocality",
  "indicatif",
+ "memmap2",
  "ndarray",
+ "niffler",
  "obicompactvec",
+ "obidebruinj",
+ "obikentropy",
  "obikpartitionner",
  "obikseq",
  "obilayeredmap",
+ "obipipeline",
  "obiread",
  "obiskio",
  "obisys",
  "obitaxonomy",
+ "ptr_hash",
  "rayon",
  "serde",
  "serde_json",
@@ -1653,16 +1661,11 @@ version = "0.1.0"
 dependencies = [
  "cacheline-ef",
  "epserde",
- "indicatif",
  "memmap2",
  "niffler",
  "obicompactvec",
- "obidebruinj",
- "obikentropy",
  "obikrope",
  "obikseq",
- "obilayeredmap",
- "obipipeline",
  "obiread",
  "obiskbuilder",
  "obiskio",