refactor: rename obikpartitionner crate to obikpartition

Update Cargo manifests, dependency paths, and Rust imports across the workspace to reflect the `obikpartitionner` to `obikpartition` rename. Synchronize architecture and implementation documentation with the new module structure. Fix minor syntax issues in test assertions to ensure compilation compatibility. No behavioral or API changes are introduced.

DevDocMD/implementation/filtering.md

@@ -303,7 +303,7 @@ This parameter has no effect on presence/absence indexes (where values are alrea
 
 ## Implementation
 
-- **`obikpartitionner::filter::GroupQuorumFilter`** — implements `KmerFilter`
+- **`obikpartition::filter::GroupQuorumFilter`** — implements `KmerFilter`
   using pre-computed ingroup and outgroup index vectors. The heavy logic
   (predicate parsing, three-value evaluation, genome classification) happens
   once before any iteration; each k-mer row evaluation is a simple index
@@ -314,7 +314,7 @@ This parameter has no effect on presence/absence indexes (where values are alrea
   `UnitigArgs`. `FilterArgs::build_filters()` returns a ready-to-use filter
   list.
 
-- **`obikpartitionner::KmerPartition::iter_partition_kmers`** — accepts
+- **`obikpartition::KmerPartition::iter_partition_kmers`** — accepts
   `filters: &[Box<dyn KmerFilter>]` and applies them per-kmer before invoking
   the callback. `filter`, `dump`, and `unitig` all go through this single
   entry point.

DevDocMD/implementation/merge.refs.md

@@ -4,8 +4,8 @@
 ## Code couvert
 
 - `obikindex/src/merge.rs` — `KmerIndex::merge()`, validation de compatibilité d'évidence, `validate_evidence_compat()`
-- `obikpartitionner/src/merge_layer.rs` — `merge_partition()`, construction de la nouvelle layer, paramètre `block_bits`
-- `obikpartitionner/src/rebuild_layer.rs` — `rebuild_partition()`, paramètre `block_bits`
+- `obikpartition/src/merge_layer.rs` — `merge_partition()`, construction de la nouvelle layer, paramètre `block_bits`
+- `obikpartition/src/rebuild_layer.rs` — `rebuild_partition()`, paramètre `block_bits`
 - `obilayeredmap/src/layer.rs` — `Layer::append_genome_column()` (PersistentCompactIntMatrix et PersistentBitMatrix)
 - `obicompactvec/src/intmatrix.rs` — `append_column` pour PersistentCompactIntMatrix
 - `obicompactvec/src/bitmatrix.rs` — `append_column` pour PersistentBitMatrix

DevDocMD/implementation/mphf.md

@@ -6,7 +6,7 @@ Kmer indexing per partition proceeds in two phases. The separation is necessary
 
 ### Phase 1 — provisional MPHF + kmer spectrum
 
-Implemented in `obikpartitionner::KmerPartition::count_kmer()` → `count_partition()`.
+Implemented in `obikpartition::KmerPartition::count_kmer()` → `count_partition()`.
 
 1. **External sort**: read the dereplicated superkmer file; extract the raw `u64` canonical kmer value for every kmer of every superkmer. Sort in RAM-bounded chunks (adaptive budget: 40% of available RAM ÷ n_threads, minimum 1 M kmers per chunk), then k-way merge with inline dedup. Result: `sorted_unique.bin` — a flat array of f0 distinct sorted `u64` values. Exact kmer count f0 is known at this point.
 2. **Build provisional MPHF** (ptr_hash, same configuration as phase 2) over `sorted_unique.bin` using `new_from_par_iter`. Delete `sorted_unique.bin` immediately after. Persist to `mphf1.bin`.
@@ -148,7 +148,7 @@ MphfLayer::build_approx_evidence(dir, b, z)
 
 There is no `build_evidence` dispatch wrapper. Callers choose the appropriate post-hoc build directly.
 
-In `obikpartitionner`, `build_index_layer` receives `block_bits: u8` from `IndexConfig::block_bits` and forwards it directly to `Layer::build` and `Layer::build_approx_evidence`.
+In `obikpartition`, `build_index_layer` receives `block_bits: u8` from `IndexConfig::block_bits` and forwards it directly to `Layer::build` and `Layer::build_approx_evidence`.
 
 ### Membership verification
 

DevDocMD/implementation/mphf.refs.md

@@ -4,7 +4,7 @@
 ## Code couvert
 
 - `obilayeredmap/src/mphf_layer.rs` — type Mphf (PtrHash + CubicEps + CachelineEfVec + Xx64), construction en 2 passes, `build()`, `build_exact_evidence()`, `build_approx_evidence()`, `build_evidence()`
-- `obikpartitionner/src/index_layer.rs` — `build_index_layer()` avec passage de `block_bits`
+- `obikpartition/src/index_layer.rs` — `build_index_layer()` avec passage de `block_bits`
 
 ## Notes
 

DevDocMD/implementation/obipipeline.refs.md

@@ -9,5 +9,5 @@
 ## Notes
 
 Document stable (librairie générique, peu de risque de dérive).
-Vérifier si `obipipeline` est toujours utilisé dans la phase scatter de `obikpartitionner`
+Vérifier si `obipipeline` est toujours utilisé dans la phase scatter de `obikpartition`
 ou s'il a été remplacé par Rayon dans certains chemins.

DevDocMD/implementation/partition_layer_cache.md

@@ -16,7 +16,7 @@ explicitly, since two of the names below are misleading.
   but it holds the *whole* multi-partition structure below — the name
   suggests "one partition", the value is all of them.
 - **Partition, the collection (not one partition)** =
-  `obikpartitionner::KmerPartition`. Despite the singular name, this owns
+  `obikpartition::KmerPartition`. Despite the singular name, this owns
   *every* partition of the index: `root_path`, `n_partitions`, and
   per-partition accessors that all take an explicit index `i`
   (`partition_dir(i)`, `index_dir(i)`, `layer_dir(i, l)`,
@@ -95,7 +95,7 @@ auto-detection" turns up three unrelated implementations:
 |---|---|---|---|
 | `Layer<D>` | `obilayeredmap` | one layer, `D` fixed at compile time | held alive by whoever owns the `Layer`, no policy of its own |
 | `Mat` | `obikphylo::siblings::cache` | one layer, format resolved per instance from an enum of 3 `Layer<D>` variants | yes, via `PartitionCache` |
-| `QueryLayer` | `obikpartitionner::query_layer` | one layer, `(MphfLayer, PersistentBitMatrix\|PersistentCompactIntMatrix)` pair, bypasses `Layer<D>` entirely | **no** — opened fresh inside `query_partition_with` on every call |
+| `QueryLayer` | `obikpartition::query_layer` | one layer, `(MphfLayer, PersistentBitMatrix\|PersistentCompactIntMatrix)` pair, bypasses `Layer<D>` entirely | **no** — opened fresh inside `query_partition_with` on every call |
 
 `query_partition_with` is `obikmer query`'s normal query path — the one
 most exposed to repeated cross-partition lookups — and it is the one with
@@ -164,7 +164,7 @@ Established in discussion, not yet coded:
   `open_data`/`layer_dir` — see git history around 2026-08-20). One
   `LayeredMap<D>` (or its heterogeneous-`D` successor) = one partition.
 - Nobody currently owns "the collection of partitions" as reusable state.
-  `obikpartitionner::KmerPartition` is the closest candidate — it already
+  `obikpartition::KmerPartition` is the closest candidate — it already
   owns `n_partitions()`/`part_dir(i)` — but today it is a pure
   config/path resolver, not a state holder: `dereplicate`, `count_kmer`,
   `obikindex`'s `distance.rs`/`stats.rs`, and
@@ -182,9 +182,9 @@ Established in discussion, not yet coded:
 2. A cache spanning multiple partitions, keeping (2)'s layer type open per
    partition per layer, for the whole lifetime of a long-running command —
    generalising `PartitionCache` minus its sibling-specific parts
-   (`fast_mode`, `find_presence_batch`) — living in `obikpartitionner`
+   (`fast_mode`, `find_presence_batch`) — living in `obikpartition`
    (owner of the partition dimension) and built on top of (1).
-3. `obikpartitionner::query_partition_with` — the normal query path,
+3. `obikpartition::query_partition_with` — the normal query path,
    currently uncached — becomes a consumer of (2), not just
    `obikphylo::PartitionCache`.
 
@@ -198,7 +198,7 @@ real number behind it for this codebase's scale).
 
 Groundwork for (1)/(2), landed ahead of the design itself:
 
-- `KmerPartition` (`obikpartitionner`) gained `partition_dir`/`index_dir`/
+- `KmerPartition` (`obikpartition`) gained `partition_dir`/`index_dir`/
   `layer_dir` as the single source of truth for a partition's on-disk
   layout, replacing per-module duplicated `const INDEX_SUBDIR: &str =
   "index"` (7 copies) and ad hoc path joins — including one found
@@ -266,7 +266,7 @@ storage decisions, now a *third* copy of the same logic to keep in sync)
   `Mat::open` already reads the result back in the sibling-annex path.
   Stale comment, not corrected.
 - **Retracted (2026-08-20)**: an earlier pass through this doc claimed
-  `obikpartitionner::query_layer::QueryLayer::open` had no sparse-format
+  `obikpartition::query_layer::QueryLayer::open` had no sparse-format
   detection and would silently corrupt reads on a `pack --sparse`d layer.
   False — `PersistentBitMatrix` (`obicompactvec::bitmatrix::persistent`)
   is a 4-way enum (`Columnar`/`Packed`/`Sparse`/`Implicit`), not 3-way as

DevDocMD/implementation/pipeline.refs.md

@@ -3,12 +3,12 @@
 
 ## Code couvert
 
-- `obikpartitionner/src/partition.rs` — estimation des paramètres (phase 0)
+- `obikpartition/src/partition.rs` — estimation des paramètres (phase 0)
 - `obiskbuilder/src/iter.rs` — scatter : filtre entropie, extraction superkmers, routage partition (phase 1)
-- `obikpartitionner/src/filter.rs` — déduplication bucket-sort (phase 2)
-- `obikpartitionner/src/kmer_sort.rs` — tri externe + agrégation de comptages (phase 3)
+- `obikpartition/src/filter.rs` — déduplication bucket-sort (phase 2)
+- `obikpartition/src/kmer_sort.rs` — tri externe + agrégation de comptages (phase 3)
 - `obidebruinj/src/debruijn.rs` — graphe De Bruijn, extraction des unitigs (phase 5)
-- `obikpartitionner/src/index_layer.rs` — construction MPHF + évidence (phase 6), paramètre `block_bits`
+- `obikpartition/src/index_layer.rs` — construction MPHF + évidence (phase 6), paramètre `block_bits`
 - `obikindex/src/index.rs` — `build_layers()`, `dereplicate_and_count()`
 
 ## Notes