feat: introduce packed matrix storage and layer metadata

Unifies bit and integer matrix storage into `PersistentBitMatrix` and `PersistentCompactIntMatrix` enums, supporting both columnar and memory-mapped single-file layouts. Introduces `LayerMeta` to persist layer dimensions as `layer_meta.json`, enabling correct initialization of implicit presence matrices. Adds CLI commands (`pack` and `--upgrade-index`) to convert existing columnar indices to the compact format and backfill missing metadata. Updates partitionner and layered map logic to use the new persistent builders, optimized memory allocation, and auto-detected storage backends.

src/obikindex/src/merge.rs

@@ -196,6 +196,16 @@ impl KmerIndex {
             rep.push(t.stop());
         }
 
+        // ── Pack matrices after merge ─────────────────────────────────────────
+        {
+            let t = Stage::start("pack");
+            let pb = spinner("pack — consolidating column files …");
+            let dst2 = KmerIndex::open(output)?;
+            dst2.pack_matrices()?;
+            pb.finish_and_clear();
+            rep.push(t.stop());
+        }
+
         // Re-open to get the updated state.
         KmerIndex::open(output)
     }