diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2180f0d..de226e6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -20,13 +20,13 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
-      - name: Checkout code (2nd)
+      - name: Checkout code (2nd) - to test extra-dirs option
         uses: actions/checkout@v4
         with:
           repository: depends-on/depends-on-action
           path: second
 
-      - name: Checkout code (3rd)
+      - name: Checkout code (3rd) - to test extra-dirs option
         uses: actions/checkout@v4
         with:
           repository: depends-on/depends-on-action
@@ -34,6 +34,7 @@ jobs:
 
       - name: Inject dependent Pull Requests
         uses: ./
+        id: inject_deps
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           extra-dirs: depends-on-action/second depends-on-action/third
diff --git a/depends_on_stage2 b/depends_on_stage2
index b3f7a30..bf9483a 100755
--- a/depends_on_stage2
+++ b/depends_on_stage2
@@ -141,6 +141,9 @@ def main(check_mode):
     real_extra_dirs = []
     for extra_dir in data["extra_dirs"]:
         real_extra_dir = os.path.realpath(extra_dir)
+        if not check_mode:
+            unshallow(real_extra_dir, data["main_branch"])
+            merge_main_branch(real_extra_dir, data["main_branch"])
         if not os.path.isdir(real_extra_dir):
             log(f"Extra directory {real_extra_dir} does not exist.")
             return 1