diff --git a/eks_automation/app.py b/eks_automation/app.py
index c692b4d..6da7e8e 100644
--- a/eks_automation/app.py
+++ b/eks_automation/app.py
@@ -484,12 +484,12 @@ def commit_repository_contents(self, repo_name, work_dir, commit_message, branch
                     "sha": blob_sha
                 })
         
-        # Try to get the latest commit SHA for the branch
-        # If it doesn't exist, we'll create it
+        # Try to get the latest commit SHA from the base branch
+        base_branch = "main"  # Always use main as base when creating new branches
         try:
-            latest_commit_sha = self.get_reference_sha(repo_name, f"heads/{target_branch}")
-            latest_commit = self.get_commit(repo_name, latest_commit_sha)
-            base_tree_sha = latest_commit["tree"]["sha"]
+            base_commit_sha = self.get_reference_sha(repo_name, f"heads/{base_branch}")
+            base_commit = self.get_commit(repo_name, base_commit_sha)
+            base_tree_sha = base_commit["tree"]["sha"]
         except Exception:
             # If we can't get the reference, assume it's a new repo with no commits
             base_tree_sha = None
@@ -504,7 +504,7 @@ def commit_repository_contents(self, repo_name, work_dir, commit_message, branch
                 repo_name, 
                 commit_message, 
                 new_tree_sha, 
-                [latest_commit_sha]
+                [base_commit_sha]
             )
         else:
             # If it's a new repo, create the first commit
@@ -517,18 +517,25 @@ def commit_repository_contents(self, repo_name, work_dir, commit_message, branch
         
         # Update or create the reference to point to the new commit
         try:
+            # Try to update existing branch
             self.update_reference(
                 repo_name, 
                 f"heads/{target_branch}", 
                 new_commit_sha
             )
         except Exception:
-            # If the reference doesn't exist, create it
-            self.create_reference(
-                repo_name, 
-                f"refs/heads/{target_branch}", 
-                new_commit_sha
-            )
+            # If the branch doesn't exist, create it
+            try:
+                self.create_reference(
+                    repo_name, 
+                    f"refs/heads/{target_branch}", 
+                    new_commit_sha
+                )
+            except Exception as e:
+                # If we still can't create the branch, something is wrong
+                error_message = f"Failed to create or update branch {target_branch} for {repo_name}: {str(e)}"
+                logger.error(error_message)
+                raise Exception(error_message)
         
         return target_branch
 
diff --git a/eks_automation/tests/test_github_client_integration.py b/eks_automation/tests/test_github_client_integration.py
index afe0587..7b24c33 100644
--- a/eks_automation/tests/test_github_client_integration.py
+++ b/eks_automation/tests/test_github_client_integration.py
@@ -126,6 +126,7 @@ def test_branch_operations(self, temp_repo_name, cleanup_repo):
         
         # Create a test file in main branch
         with tempfile.TemporaryDirectory() as work_dir:
+            # Initial commit on main branch
             main_file = os.path.join(work_dir, "test.txt")
             with open(main_file, "w") as f:
                 f.write("main branch content")
@@ -136,10 +137,15 @@ def test_branch_operations(self, temp_repo_name, cleanup_repo):
                 "Initial commit on main"
             )
             
-            # Create and switch to a new branch
+            # Create and switch to a test branch
             test_branch = "test-branch"
-            shutil.rmtree(work_dir)
-            os.makedirs(work_dir)
+            # Clean directory for test branch changes
+            for file in os.listdir(work_dir):
+                file_path = os.path.join(work_dir, file)
+                if os.path.isfile(file_path):
+                    os.unlink(file_path)
+                elif os.path.isdir(file_path):
+                    shutil.rmtree(file_path)
             
             # Create different content in test branch
             with open(main_file, "w") as f:
@@ -152,14 +158,18 @@ def test_branch_operations(self, temp_repo_name, cleanup_repo):
                 branch=test_branch
             )
             
-            # Verify main branch content
-            main_output = os.path.join(work_dir, "main")
+            # Clone and verify main branch content
+            main_output = os.path.join(work_dir, "clone-main")
+            os.makedirs(main_output, exist_ok=True)
             self.client.clone_repository_contents(repo_name, main_output, branch="main")
+            
             with open(os.path.join(main_output, "test.txt")) as f:
-                assert f.read() == "main branch content"
+                assert f.read().strip() == "main branch content"
             
-            # Verify test branch content
-            test_output = os.path.join(work_dir, "test")
+            # Clone and verify test branch content
+            test_output = os.path.join(work_dir, "clone-test")
+            os.makedirs(test_output, exist_ok=True)
             self.client.clone_repository_contents(repo_name, test_output, branch=test_branch)
+            
             with open(os.path.join(test_output, "test.txt")) as f:
-                assert f.read() == "test branch content"
+                assert f.read().strip() == "test branch content"