diff --git a/setup_main_tex_file.py b/setup_main_tex_file.py
index 8cd5380..d423b0f 100755
--- a/setup_main_tex_file.py
+++ b/setup_main_tex_file.py
@@ -80,7 +80,8 @@ def git_integration(func):
 
             author = repo.default_signature
             committer = author
-
+            
+            repo.checkout('refs/heads/master')
             index = repo.index
             for fp in master_add_paths:
                 index.add(fp)
@@ -95,6 +96,7 @@ def git_integration(func):
                     tree,
                     parents)
 
+            repo.checkout(f'refs/heads/{branch_name}')
             for fp in branch_add_paths:
                 index.add(fp)
             index.write()