feat: add sparse on-disk format for presence matrices

The index packing API now accepts a `sparse` parameter to generate `PersistentSparseBitMatrix` files alongside existing dense matrices. The sibling cache automatically detects this format via an `is_multi.prsb` marker file and routes queries identically to the dense variant. A new `--sparse` CLI flag exposes the option, with tests verifying end-to-end pipeline correctness and storage equivalence.

docmd/architecture/siblings.md

@@ -496,3 +496,59 @@ Also still deferred, unchanged from the implementation plan: full Alanko
 et al. subset-hierarchy compression (only the exact-duplicate special case
 is built), a sparse `PersistentCompactIntMatrix` (count matrices), and
 BRWT-style column-correlation exploitation.
+
+## Wired into `pack` and the sibling-annex build path (2026-08-15)
+
+`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
+  (`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
+  `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
+  the same directory, assert `n_cols`/`sub_matrix`/`find_slot` agree.
+  (This test must stay at `k=4` with mutually non-colliding canonical
+  4-mers across its input sequences — `K`/`M` are process-wide
+  `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.)
+- **`obikphylo::siblings::cache::Mat`** gained a third variant,
+  `SparsePresence(Layer<PersistentSparseBitMatrix>)`, alongside `Count`
+  and `Presence` — every method (`find_slot`, `index_batch`,
+  `iter_minorants_batch`, `n_cols`, `fill_sub_matrix_carries`) dispatches
+  to it identically to `Presence`, since both go through the same generic
+  `Layer<D>` code. `PartitionCache::build` picks the variant per layer by
+  checking for `presence/is_multi.prsb` (the sparse format's own marker
+  file, see the design section above) before falling back to the dense
+  open path.
+- **`pack_sparse_bit_matrix`** (new, `obicompactvec::bitmatrix::sparse`):
+  `pack --sparse`'s entry point. Idempotent (checks `is_multi.prsb`
+  first); packs to dense `matrix.pbmx` first if that hasn't happened yet
+  (the dense→sparse transpose needs random row access, which only the
+  packed/columnar dense forms give), then `build_from_dense`s the sparse
+  form into the same directory and deletes `matrix.pbmx` — old-format
+  files are removed only after the new format is fully written, mirroring
+  `pack_bit_matrix`'s own crash-safety convention.
+- **CLI**: `obikmer pack --sparse` threads a `sparse: bool` through
+  `KmerIndex::pack_matrices` (all other call sites — `select`, `merge`,
+  `finalize_indexed` — pass `false`, unchanged dense behaviour). Count
+  matrices are untouched by `--sparse` (no sparse `PersistentCompactIntMatrix`
+  — see "still deferred" above).
+- **End-to-end coverage**: `obikphylo::siblings::tests::
+  sibling_annex_works_after_pack_sparse` builds a two-genome index, packs
+  it `--sparse`, asserts `is_multi.prsb` exists, then runs
+  `build_sibling_annex` and checks the resulting `FamilyMask`s match the
+  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.
+
+Full workspace `cargo test` (all crates, unit + doc tests) green after
+this change.