fix sync again

Author: daquinteroflex

.github/workflows/tidy3d-docs-sync-readthedocs-repo.yml

@@ -83,10 +83,18 @@ jobs:
           # Get list of submodules
           git config --file .gitmodules --get-regexp path | awk '{ print $2 }' > /tmp/submodule_paths.txt
 
+          # Remove each submodule from git's index (but keep the files)
+          while IFS= read -r submodule_path; do
+            if [ -d "$submodule_path" ]; then
+              echo "Removing submodule from index: $submodule_path"
+              git rm --cached "$submodule_path" || true
+            fi
+          done < /tmp/submodule_paths.txt
+
           # Remove .git directories from submodules (converts them to regular directories)
           while IFS= read -r submodule_path; do
             if [ -d "$submodule_path/.git" ]; then
-              echo "Flattening submodule: $submodule_path"
+              echo "Removing .git directory: $submodule_path/.git"
               rm -rf "$submodule_path/.git"
             fi
           done < /tmp/submodule_paths.txt
@@ -96,8 +104,16 @@ jobs:
           git config --remove-section submodule.docs/notebooks || true
           git config --remove-section submodule.docs/faq || true
 
-          # Stage all changes (submodule content will now be tracked as regular files)
-          git add -A
+          # Add submodule content back as regular files
+          while IFS= read -r submodule_path; do
+            if [ -d "$submodule_path" ]; then
+              echo "Adding submodule content as regular files: $submodule_path"
+              git add "$submodule_path/"
+            fi
+          done < /tmp/submodule_paths.txt
+
+          # Stage removal of .gitmodules
+          git add .gitmodules || true
 
           # Configure git user for commit
           git config user.name "github-actions[bot]"