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.

src/obikindex/src/index.rs

@@ -122,7 +122,7 @@ impl KmerIndex {
         fs::File::create(output.join(SENTINEL_INDEXED)).map_err(OKIError::Io)?;
         let idx = KmerIndex::open(output)?;
         let t_pack = Stage::start("pack");
-        idx.pack_matrices()?;
+        idx.pack_matrices(false)?;
         rep.push(t_pack.stop());
         Ok(idx)
     }
@@ -274,8 +274,14 @@ 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.
-    pub fn pack_matrices(&self) -> OKIResult<()> {
-        use obicompactvec::{pack_bit_matrix, pack_compact_int_matrix};
+    ///
+    /// If `sparse` is set, presence matrices go one step further, from the
+    /// dense `.pbmx` form into `obicompactvec::PersistentSparseBitMatrix`'s
+    /// on-disk format (see `docmd/architecture/siblings.md`) — count
+    /// matrices are unaffected, sparse count matrices aren't implemented
+    /// (see the sparse-matrix design plan's "Explicitly deferred").
+    pub fn pack_matrices(&self, sparse: bool) -> OKIResult<()> {
+        use obicompactvec::{pack_bit_matrix, pack_compact_int_matrix, pack_sparse_bit_matrix};
         use obilayeredmap::meta::PartitionMeta;
 
         let n = self.n_partitions();
@@ -292,7 +298,13 @@ impl KmerIndex {
                     let layer_dir = index_dir.join(format!("layer_{l}"));
                     let presence_dir = layer_dir.join("presence");
                     let counts_dir   = layer_dir.join("counts");
-                    if presence_dir.exists() { pack_bit_matrix(&presence_dir).map_err(OKIError::Io)?; }
+                    if presence_dir.exists() {
+                        if sparse {
+                            pack_sparse_bit_matrix(&presence_dir).map_err(OKIError::Io)?;
+                        } else {
+                            pack_bit_matrix(&presence_dir).map_err(OKIError::Io)?;
+                        }
+                    }
                     if counts_dir.exists()   { pack_compact_int_matrix(&counts_dir).map_err(OKIError::Io)?; }
                 }
                 Ok(())

src/obikindex/src/merge.rs

@@ -249,7 +249,7 @@ impl KmerIndex {
             let pb = spinner("pack");
             pb.set_message("consolidating column files …");
             let dst2 = KmerIndex::open(output)?;
-            dst2.pack_matrices()?;
+            dst2.pack_matrices(false)?;
             pb.finish_and_clear();
             rep.push(t.stop());
         }

src/obikindex/src/select.rs

@@ -118,7 +118,7 @@ impl KmerIndex {
         self.meta.write(&self.root_path)?;
 
         let t_pack = Stage::start("pack");
-        self.pack_matrices()?;
+        self.pack_matrices(false)?;
         rep.push(t_pack.stop());
         Ok(())
     }