diff --git a/app/assets/javascripts/ide/stores/mutations.js b/app/assets/javascripts/ide/stores/mutations.js
index a8b0aad25fa..bc6e23fc386 100644
--- a/app/assets/javascripts/ide/stores/mutations.js
+++ b/app/assets/javascripts/ide/stores/mutations.js
@@ -199,7 +199,7 @@ export default {
 
     entry.deleted = true;
 
-    parent.tree.splice(parent.tree.findIndex(f => f.path === entry.path), 1);
+    parent.tree = parent.tree.filter(f => f.path !== entry.path);
 
     if (entry.type === 'blob') {
       state.changedFiles = state.changedFiles.concat(entry);
diff --git a/app/assets/javascripts/ide/stores/utils.js b/app/assets/javascripts/ide/stores/utils.js
index 6d4941e9c32..fba1f70bf6c 100644
--- a/app/assets/javascripts/ide/stores/utils.js
+++ b/app/assets/javascripts/ide/stores/utils.js
@@ -121,17 +121,12 @@ export const commitActionForFile = file => {
   return 'update';
 };
 
-export const getCommitFiles = (stagedFiles, deleteTree = false) =>
+export const getCommitFiles = stagedFiles =>
   stagedFiles.reduce((acc, file) => {
     if (file.moved) return acc;
 
-    if ((file.deleted || deleteTree || file.prevPath) && file.type === 'tree') {
-      return acc.concat(getCommitFiles(file.tree, true));
-    }
-
     return acc.concat({
       ...file,
-      deleted: deleteTree || file.deleted,
     });
   }, []);