MacOS fix stow secrets issue

Scripts/setup.sh

@@ -18,10 +18,34 @@ handle_reboot_marker() {
 }
 
 sync_repo_managed_secret_file() {
+    local home_secret_resolved repo_secret_resolved
+
     mkdir -p "$(dirname "$REPO_SECRET_FILE")"
 
     if [ -L "$HOME_SECRET_FILE" ]; then
-        return 0
+        home_secret_resolved="$(python3 -c 'import os,sys; print(os.path.realpath(sys.argv[1]))' "$HOME_SECRET_FILE")"
+        repo_secret_resolved="$(python3 -c 'import os,sys; print(os.path.realpath(sys.argv[1]))' "$REPO_SECRET_FILE")"
+
+        if [ "$home_secret_resolved" = "$repo_secret_resolved" ]; then
+            return 0
+        fi
+
+        if [ -f "$home_secret_resolved" ]; then
+            if [ ! -f "$REPO_SECRET_FILE" ] || [ ! -s "$REPO_SECRET_FILE" ]; then
+                cp "$home_secret_resolved" "$REPO_SECRET_FILE"
+                rm -f "$HOME_SECRET_FILE"
+                return 0
+            fi
+
+            if cmp -s "$home_secret_resolved" "$REPO_SECRET_FILE"; then
+                rm -f "$HOME_SECRET_FILE"
+                return 0
+            fi
+        fi
+
+        echo "Conflict: $HOME_SECRET_FILE points to a different secret file than $REPO_SECRET_FILE."
+        echo "Please merge them manually, then rerun the command."
+        exit 1
     fi
 
     if [ -f "$HOME_SECRET_FILE" ]; then