Fixed preventing git submodules from being committed

- because we now ignore git submodule changes, they didn't show up in
  `git diff --cached...`, so it was possible to get submodules to be
  committed
- you can re-enable submodules to be shown with `--ignore-submodules=none`
- this implements that
- we never want to allow submodules to be committed, so I've removed the
  prompt for faster feedback

.github/hooks/pre-commit

@@ -17,11 +17,11 @@ fi
 green='\033[0;32m'
 no_color='\033[0m'
 grey='\033[0;90m'
-
+red='\033[0;31m'
 
 ROOT_DIR=$(git rev-parse --show-cdup)
 SUBMODULES=$(grep path ${ROOT_DIR}.gitmodules | sed 's/^.*path = //')
-MOD_SUBMODULES=$(git diff --cached --name-only | grep -F "$SUBMODULES")
+MOD_SUBMODULES=$(git diff --cached --name-only --ignore-submodules=none | grep -F "$SUBMODULES")
 
 echo -e "Checking submodules ${grey}(pre-commit hook)${no_color} "
 
@@ -37,16 +37,8 @@ if [[ -n "$MOD_SUBMODULES" ]]; then
         echo -e "\t${green}modified:\t$SUB${no_color}"
     done
     echo
-    echo -n -e "Continue with commit? ${grey}(N|y)${no_color} "
-    read -n 1 reply </dev/tty
-    echo
-    if [[ "$reply" == "y" || "$reply" == "Y" ]]; then
-        echo "Permitting submodules to be committed..."
-        exit 0
-    else
-        echo "Aborting commit due to submodule update."
-        exit 1
-    fi
+    echo -e "${red}Aborting commit due to submodule update. Please unstage the submodule(s) and commit again.${no_color}"
+    exit 1
 else
     echo "No submodules in commit, continuing..."
     exit 0