Add configurable sparsity flag to index finalization and merge CLI

Extends `KmerIndex::finalize_indexed` to accept a `sparse` boolean parameter, enabling control over whether output presence matrices are packed in a compact sparse format or stored densely. The merge command now exposes a `--dense` flag to invert this setting, defaulting to the existing sparse representation. Call sites in select and rebuild modules pass `false` to preserve current behavior. A benchmark lock file is also added for dependency tracking.

src/obikindex/src/index/builder.rs

@@ -52,9 +52,10 @@ pub trait IndexBuilder: Sized {
 
     /// Mark `output` as fully indexed, pack its column matrices, and reopen it.
     ///
-    /// Shared tail of the `select`/`rebuild` construction paths, once their
-    /// partitions have been written.
-    fn finalize_indexed<P: AsRef<Path>>(output: P, rep: &mut Reporter) -> OKIResult<Self>;
+    /// Shared tail of the `select`/`rebuild`/`merge` construction paths,
+    /// once their partitions have been written. `sparse` selects the
+    /// on-disk presence-matrix format (see `pack_matrices`).
+    fn finalize_indexed<P: AsRef<Path>>(output: P, rep: &mut Reporter, sparse: bool) -> OKIResult<Self>;
 
     /// Current construction state, read fresh from `index.meta` (see
     /// `DevDocMD/implementation/partition_layer_cache.md`, "(11)" — no
@@ -99,12 +100,12 @@ impl IndexBuilder for KmerIndex {
         Ok(idx)
     }
 
-    fn finalize_indexed<P: AsRef<Path>>(output: P, rep: &mut Reporter) -> OKIResult<Self> {
+    fn finalize_indexed<P: AsRef<Path>>(output: P, rep: &mut Reporter, sparse: bool) -> OKIResult<Self> {
         let output = output.as_ref();
         let idx = KmerIndex::open(output)?;
         idx.meta.mark_indexed().map_err(OKIError::Io)?;
         let t_pack = Stage::start("pack");
-        idx.pack_matrices(false)?;
+        idx.pack_matrices(sparse)?;
         rep.push(t_pack.stop());
         Ok(idx)
     }