diff --git a/src/obikmerge/src/merge.rs b/src/obikmerge/src/merge.rs
index b204759b..62ff8bef 100644
--- a/src/obikmerge/src/merge.rs
+++ b/src/obikmerge/src/merge.rs
@@ -514,15 +514,35 @@ fn choose_base(sources: &[&KmerIndex], src_genomes: &[Vec<GenomeInfo>], mode: Me
         .unwrap()
 }
 
+/// Copies `src` (the base source's whole `partitions/` tree) into `dst` at
+/// bootstrap, before any actual merging happens. `merge_partition` (right
+/// after) widens the pre-existing layers' `presence`/`counts` matrix files
+/// in place — appending the new sources' genome columns — so those must
+/// stay real, independent copies; everything else in a layer directory
+/// (`mphf.bin`/`unitigs.bin`/`evidence.bin`/`unitigs.bin.idx`/
+/// `fingerprint.bin`/`layer_meta.json`) is never touched again once copied
+/// here, exactly the same "kmer identity vs. data matrix" split
+/// `obikselect::select_layer::copy_layer_files` makes — so those are safe
+/// to hard-link instead, avoiding a second full copy of a layer's largest
+/// files on a big index. Falls back to a real copy per file when linking
+/// itself fails (e.g. `src`/`dst` on different filesystems).
 fn copy_dir_all(src: &Path, dst: &Path) -> io::Result<()> {
+    copy_dir_all_inner(src, dst, false)
+}
+
+fn copy_dir_all_inner(src: &Path, dst: &Path, force_copy: bool) -> io::Result<()> {
     fs::create_dir_all(dst)?;
     for entry in fs::read_dir(src)? {
         let entry = entry?;
         let src_path = entry.path();
         let dst_path = dst.join(entry.file_name());
         if src_path.is_dir() {
-            copy_dir_all(&src_path, &dst_path)?;
-        } else {
+            // Once inside a `presence`/`counts` matrix subdirectory, every
+            // file below it — however deep — must be a real copy too.
+            let name = entry.file_name();
+            let is_matrix_dir = name == "presence" || name == "counts";
+            copy_dir_all_inner(&src_path, &dst_path, force_copy || is_matrix_dir)?;
+        } else if force_copy || fs::hard_link(&src_path, &dst_path).is_err() {
             fs::copy(&src_path, &dst_path)?;
         }
     }