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/obikmerge/src/merge.rs

@@ -45,6 +45,7 @@ pub struct Merge<'a> {
     mode: MergeMode,
     force: bool,
     rename_duplicates: bool,
+    sparse: bool,
     reporter: Reporter,
     on_progress: Option<Box<dyn FnMut(Progress) + Send + 'a>>,
 }
@@ -57,6 +58,7 @@ impl<'a> Merge<'a> {
             mode,
             force: false,
             rename_duplicates: false,
+            sparse: true,
             reporter: Reporter::new(),
             on_progress: None,
         }
@@ -76,6 +78,13 @@ impl<'a> Merge<'a> {
         self
     }
 
+    /// Pack the merged output's presence matrices in the compact sparse
+    /// format rather than dense (default: `true`).
+    pub fn sparse(mut self, v: bool) -> Self {
+        self.sparse = v;
+        self
+    }
+
     /// Progress callback, called once per completed partition.
     pub fn on_progress(mut self, cb: impl FnMut(Progress) + Send + 'a) -> Self {
         self.on_progress = Some(Box::new(cb));
@@ -322,7 +331,7 @@ impl Algorithm for Merge<'_> {
 
         // ── Finalize: pack matrices, mark indexed, reopen ──────────────────────
         let t = Stage::start("finalize");
-        let dst = KmerIndex::finalize_indexed(&output, &mut self.reporter)?;
+        let dst = KmerIndex::finalize_indexed(&output, &mut self.reporter, self.sparse)?;
         self.reporter.push(t.stop());
 
         Ok(dst)