feat: enable index resumption and enforce directory creation

The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.

DevDocMD/architecture/siblings.md

@@ -17,7 +17,7 @@ one-way function, not an invertible bijection with a stored inverse. Any
 method that reconstructs a kmer from a bare slot number is wrong by
 construction, regardless of the mechanism used (MPHF re-hash, or evidence
 decode + direct unitig read). See `MphfLayer::kmer_at`
-(`obilayeredmap/src/mphf_layer.rs`) — flagged for removal, currently called
+(`obikindex/src/layer/mphf_layer.rs`) — flagged for removal, currently called
 from `obikphylo/siblings/build.rs` and `family_scan.rs` (since removed — see
 "Pending work" status below).
 
@@ -70,7 +70,7 @@ partition is unknown) and must keep going through
 ## Pending work — done
 
 The plan above shipped: `obikphylo` (a new crate — phylo-domain extension
-traits over `obikindex::KmerIndex`/`obilayeredmap::Layer<D>`, replacing the
+traits over `obikindex::KmerIndex`/`obikindex::layer::Layer<D>`, replacing the
 old `obikindex::siblings` module) builds and reads the annex purely in
 iteration order (`SiblingLayerExt::iter_siblings`/`iter_minorants`, both with
 batch variants, mirroring `Layer<D>`'s own `KmerIter`/`KmerBatchIter`
@@ -652,13 +652,13 @@ BRWT-style column-correlation exploitation.
 `PersistentSparseBitMatrix` went from a validated but unused type to a
 real, selectable on-disk format:
 
-- **Generic `Layer<D>`**: `obilayeredmap::Layer<D>`'s presence-only methods
+- **Generic `Layer<D>`**: `obikindex::layer::Layer<D>`'s presence-only methods
   (`n_cols`, `sub_matrix`, `fill_sub_matrix`) are generic over any
   `D: LayerData<Item = Box<[bool]>> + BinaryMatrix`, not hardcoded to
   `PersistentBitMatrix` — `PersistentSparseBitMatrix` implements
   `LayerData` (`open`/`read`) the same way. `find_slot`/`index_batch` were
   already generic over any `D: LayerData`, so they needed no change.
-  Verified by `obilayeredmap`'s
+  Verified by `obikindex::layer`'s
   `presence_layer_generic_over_sparse_matches_dense` test: build a dense
   presence layer, convert it to sparse via `build_from_dense`, open both
   as `Layer<PersistentBitMatrix>`/`Layer<PersistentSparseBitMatrix>` on
@@ -668,7 +668,7 @@ real, selectable on-disk format:
   `AtomicUsize`s in test builds, not thread-local, so a test using a
   different `k` races every other test in the same crate binary; a k=11
   version of this test passed alone but failed under the full
-  `obilayeredmap` suite for exactly that reason before being fixed.)
+  `obikindex::layer` suite for exactly that reason before being fixed.)
 - **`obikphylo::siblings::cache::Mat`** gained a third variant,
   `SparsePresence(Layer<PersistentSparseBitMatrix>)`, alongside `Count`
   and `Presence` — every method (`find_slot`, `index_batch`,
@@ -698,7 +698,7 @@ real, selectable on-disk format:
   dense-path test (`sibling_annex_one_sibling_each`) exactly — proves the
   sparse format round-trips through the real build pipeline
   (`PartitionCache` sparse-detection included), not just the
-  `obicompactvec`/`obilayeredmap` unit layers below it.
+  `obicompactvec`/`obikindex::layer` unit layers below it.
 
 Full workspace `cargo test` (all crates, unit + doc tests) green after
 this change.
@@ -746,7 +746,7 @@ Replaces the "four independent scans" problem above and implements
   (activation: either given; defaults `1.0`/`0.5` for whichever is unset).
 
 Full workspace `cargo test` green after this change (167 unit tests in
-`obicompactvec`+`obilayeredmap`+`obikphylo` alone, plus every other
+`obicompactvec`+`obikindex::layer`+`obikphylo` alone, plus every other
 crate's suite, no regressions).
 
 **Still open, not part of this change** (per "Correction to the 'single
@@ -770,7 +770,7 @@ reproducible across two runs with warm disk cache), the opposite of
 query").
 
 **Root cause, read from source, not measured in isolation:**
-`KmerPartition::query_partition_with` (`obikpartition/src/query_layer.rs:155-220`)
+`KmerPartition::query_partition_with` (`obikindex/src/partition/query_layer.rs:155-220`)
 is architecturally column-major: stage 2 walks `for g in 0..n_cols { for
 slot in hit_slots { layer.col_value(g, slot) } }`, documented (correctly)
 as the right locality strategy for the packed/columnar formats, where
@@ -914,7 +914,7 @@ replaces.
   `PersistentCompactIntMatrix::nonzero_iter` added the same way (counts
   not excluded, per the earlier ask) — no native low-effort case, since no
   sparse count format exists, but on the same primitive, ready for one.
-- `KmerPartition::query_partition_with` (`obikpartition/src/query_layer.rs`):
+- `KmerPartition::query_partition_with` (`obikindex/src/partition/query_layer.rs`):
   stage 2's column-major `for g { for slot { col_value } }` replaced by one
   `layer.nonzero_iter(&slot_list)` call per layer, format-agnostic.
 - Tests: `nonzero_iter_matches_dense`, `nonzero_iter_matches_row`, and —