diff --git a/depends_on/common.py b/depends_on/common.py
index 2bbfc40..d40b027 100644
--- a/depends_on/common.py
+++ b/depends_on/common.py
@@ -3,6 +3,7 @@
 import json
 import os
 import re
+import subprocess
 import sys
 import urllib.parse
 from urllib.request import Request, urlopen
@@ -347,8 +348,14 @@ def check_error(status, message):
 def command(cmd):
     "Execute a command"
     log(f"+ {cmd}")
-    ret = os.system(cmd)
-    check_error(ret == 0, f"Command failed with exit code {ret}")
+    try:
+        _ = subprocess.run(
+            cmd, shell=True, stderr=subprocess.PIPE, text=True, check=True
+        )
+    except subprocess.CalledProcessError as e:
+        log(f"Command failed with exit code {e.returncode}")
+        log(e.stderr)
+        sys.exit(1)
 
 
 def is_gerrit(change_url):
diff --git a/depends_on_stage2 b/depends_on_stage2
index 399c7e8..4b64c61 100755
--- a/depends_on_stage2
+++ b/depends_on_stage2
@@ -65,14 +65,17 @@ def extract_change(change_info, main_url, work_dir):
         )
     else:
         return extract_github_change(
-            fork_url,
-            change_info["branch"],
             main_url,
             pr_number,
             work_dir,
         )
 
 
+def extract_default_branch(work_dir) -> str:
+    "Return the default branch of the git repository in work_dir."
+    return os.popen(f"cd {work_dir} && git rev-parse --abbrev-ref HEAD").read().strip()
+
+
 def main(check_mode):
     "Main function."
 
@@ -154,6 +157,10 @@ def main(check_mode):
         # lookup if the remote of the directory is part of the depends_on
         # if yes, then we need to extract the right branch
         origin_url = extract_origin_url(real_extra_dir)
+        if not check_mode:
+            main_branch = extract_default_branch(real_extra_dir)
+            unshallow(real_extra_dir, main_branch)
+            merge_main_branch(real_extra_dir, main_branch)
         for depends_on_url in depends_on + [data["change_url"]]:
             log(f"depends_on_url: {depends_on_url} {origin_url}")
             if depends_on_url.startswith(origin_url):