Fix remove() corrupting parent indices and leaking data array

src/base.rs

@@ -122,7 +122,7 @@
         let mut tax_ids = self.tax_ids.clone();
         tax_ids.sort_unstable();
         let mut dupes = HashSet::new();
         let mut last = tax_ids.get(0).unwrap();
 
         for i in 1..tax_ids.len() {
             let cur = tax_ids.get(i).unwrap();
@@ -292,11 +292,14 @@
         self.parent_distances.remove(idx);
         self.ranks.remove(idx);
         self.names.remove(idx);
-
-        // everything after `tax_id` in parents needs to get decremented by 1
-        // because we've changed the actual array size
-        for parent in self.parent_ids.iter_mut().skip(idx + 1) {
-            if *parent > 0 {
+        self.data.remove(idx);
+
+        // all parent indices pointing to positions after the removed node must be
+        // decremented by 1, because the array shifted. This applies to every element
+        // (not just those after idx), since an out-of-order taxonomy can have parents
+        // with larger indices than their children.
+        for parent in self.parent_ids.iter_mut() {
+            if *parent > idx {
                 *parent -= 1;
             }
         }
@@ -523,6 +526,30 @@
         assert!(tax.remove("1").is_err());
     }
 
+    #[test]
+    fn remove_then_add_then_prune_preserves_nodes() {
+        use crate::edit::prune_to;
+
+        // Reproduce DEV-9780: removing a node, adding it back under a new parent,
+        // then pruning should not lose unrelated nodes or panic.
+        let mut tax = create_test_taxonomy();
+
+        // Remove "2" (Bacteria), which is a child of root and parent of "562"
+        tax.remove("2").unwrap();
+
+        // Add "2" back directly under root
+        tax.add("1", "2").unwrap();
+
+        // Prune to keep "562" (E. coli). Before the fix, "562" was unreachable
+        // from root after the remove+add, so the pruned taxonomy was empty.
+        let pruned = prune_to(&tax, &["562"], false).unwrap();
+
+        // "562" must be present and reachable
+        assert!(pruned.to_internal_index("562").is_ok());
+        // Root must be present
+        assert_eq!(Taxonomy::<&str>::root(&pruned), "1");
+    }
+
     #[test]
     fn errors_on_taxonomy_with_cycle() {
         let example = r#"{