Rename PersistentCompactIntMatrix to PersistentIntMatrix

Update all matrix type references, imports, and instantiations across
the codebase to use the new PersistentIntMatrix name. The change also
includes standardizing code formatting, such as multi-line statements
and import ordering, without altering any behavioral logic or public
API contracts.

src/obikphylo/src/matrix_store.rs

@@ -1,15 +1,15 @@
+use obicompactvec::{PersistentBitMatrix, PersistentIntMatrix};
+use obikidxcache::LayeredStore;
 use obikindex::OKIResult;
 use obikindex::layer::open_data;
-use obikidxcache::LayeredStore;
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
 
-use obikindex::load_meta;
 use obikindex::KmerIndex;
+use obikindex::load_meta;
 
 impl KmerIndex {
     /// Open all count matrices for partition `part`, one per layer.
     /// Layers without a `counts/` directory are skipped.
-    pub fn count_store(&self, part: usize) -> OKIResult<LayeredStore<PersistentCompactIntMatrix>> {
+    pub fn count_store(&self, part: usize) -> OKIResult<LayeredStore<PersistentIntMatrix>> {
         let index_dir = self.index_dir(part);
         if !index_dir.exists() {
             return Ok(LayeredStore::new(vec![]));