Implement pack CLI command for matrix packing and layer compaction

Adds the `pack` subcommand to `obikmer2` for persisting presence and count matrices in sparse or dense formats. Introduces the `compact_layer` module in `obikrebuild` to merge multiple partition layers into a single layer in-place via atomic operations. Updates dependencies across `obikdump`, `obikmer2`, and `obikrebuild` to resolve new local crate references. Shifts the architecture from multi-layer accumulation to in-place compaction, removing legacy rebuild modules.

src/obikindex/src/index/kmer_index.rs

@@ -245,14 +245,25 @@ impl KmerIndex {
     /// Reduces per-query file-open overhead from O(n_genomes) to O(1) per partition.
     /// Column files are kept in place; packed files take priority when opening.
     ///
-    /// If `sparse` is set, presence matrices go one step further, from the
-    /// dense `.pbmx` form into `obicompactvec::PersistentSparseBitMatrix`'s
-    /// on-disk format (see `DevDocMD/architecture/siblings.md`) — count
-    /// matrices are unaffected, sparse count matrices aren't implemented
-    /// (see the sparse-matrix design plan's "Explicitly deferred").
-    /// TODO: To be moved somewhere else
-    pub(crate) fn pack_matrices(&self, sparse: bool) -> OKIResult<()> {
-        use obicompactvec::{pack_bit_matrix, pack_compact_int_matrix, pack_sparse_bit_matrix};
+    /// If `sparse` is set, both matrix kinds go one step further, from their
+    /// dense single-file form into `obicompactvec`'s sparse, deduplicated
+    /// on-disk formats (`PersistentSparseBitMatrix` for presence,
+    /// `PersistentSparseCompactIntMatrix` for counts) — smaller and faster
+    /// for single-row access on real, sparse data; column-oriented access
+    /// (`--metric` distance matrices) is much slower on the sparse format.
+    ///
+    /// Public — and not moved out of this crate, despite covering the same
+    /// "maintenance operation on an already-built index" territory as
+    /// `obikrebuild` — because `finalize_indexed` calls it internally as the
+    /// shared tail of every index-building algorithm (`select`/`filter`/
+    /// `merge`), and `obikindex` cannot depend on `obikrebuild` (wrong
+    /// direction). Standalone re-packing (`obikmer2 pack`) calls this same
+    /// method directly.
+    pub fn pack_matrices(&self, sparse: bool) -> OKIResult<()> {
+        use obicompactvec::{
+            pack_bit_matrix, pack_compact_int_matrix, pack_sparse_bit_matrix,
+            pack_sparse_compact_int_matrix,
+        };
 
         let n = self.n_partitions();
         let order: Vec<usize> = (0..n).collect();
@@ -277,7 +288,11 @@ impl KmerIndex {
                         }
                     }
                     if counts_dir.exists() {
-                        pack_compact_int_matrix(&counts_dir).map_err(OKIError::Io)?;
+                        if sparse {
+                            pack_sparse_compact_int_matrix(&counts_dir).map_err(OKIError::Io)?;
+                        } else {
+                            pack_compact_int_matrix(&counts_dir).map_err(OKIError::Io)?;
+                        }
                     }
                 }
                 Ok(())