refactor: improve resource cleanup and index packing

Explicitly close file handles and remove temporary artifacts after serialization to prevent disk space leaks. Additionally, compact internal matrix structures immediately upon loading the KmerIndex to improve memory efficiency and prepare for downstream operations.

src/obicompactvec/src/bitmatrix.rs

@@ -190,6 +190,10 @@ pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> {
     file.write_all(&(n_cols as u64).to_le_bytes())?;
     for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
     for data in &col_files { file.write_all(data)?; }
+    drop(file);
+
+    for c in 0..n_cols { fs::remove_file(col_path(dir, c))?; }
+    fs::remove_file(dir.join("meta.json"))?;
     Ok(())
 }
 

src/obicompactvec/src/intmatrix.rs

@@ -293,6 +293,10 @@ pub fn pack_compact_int_matrix(dir: &Path) -> io::Result<()> {
     file.write_all(&(n_cols as u64).to_le_bytes())?;
     for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
     for data in &col_files { file.write_all(data)?; }
+    drop(file);
+
+    for c in 0..n_cols { fs::remove_file(col_path(dir, c))?; }
+    fs::remove_file(dir.join("meta.json"))?;
     Ok(())
 }
 

src/obikindex/src/rebuild.rs

@@ -112,6 +112,8 @@ impl KmerIndex {
         // Write SENTINEL_INDEXED — output is ready to use.
         fs::File::create(output.join(SENTINEL_INDEXED))?;
 
-        KmerIndex::open(output)
+        let idx = KmerIndex::open(output)?;
+        idx.pack_matrices()?;
+        Ok(idx)
     }
 }