Stop adding patches to the Git index by default

Continue adding patches to the index before doing a 3-way merge to avoid the error "file does not match index"

scripts/setup-submodule-patches.sh

@@ -4,8 +4,8 @@
 source "$(dirname "$(realpath "$0")")/internal/framework.sh"
 set_description "This configures, resets the contents of, and applies patches to the submodules in the repos directory."
 add_option "-u --update-remote" "update_remote" "Updates the submodules from their remotes before applying patches. Only \
-use this if you're trying to update the submodules to a newer version than is supported by this project. Patches will \
-be applied first with --reject, and if that fails, a 3-way merge will be attempted."
+use this if you're trying to update the submodules to a newer version than is supported by this project. If a patch \
+fails to apply, a 3-way merge will be attempted."
 parse_arguments "$@"
 
 print_info "Resetting all submodules..."
@@ -30,9 +30,9 @@ for dir in "$git_base_dir/patches/"*; do
         for patch in "$git_base_dir/patches/$subdir"/*; do
             if [[ -n "$update_remote" ]]; then
                 print_info "Applying patch $patch..."
-                if ! git apply --reject "$patch"; then
+                # Without --index, --3way will show the error "file: does not match index"
+                if ! git apply --index "$patch"; then
                     print_error "Failed to apply patch $patch! Attempting 3-way merge..."
-                    git add .
                     if ! git apply --3way "$patch"; then
                         print_error "There are merge conflicts with the patch that need to be resolved manually."
                     else
@@ -46,8 +46,6 @@ for dir in "$git_base_dir/patches/"*; do
             fi
             patch_count=$((patch_count + 1))
         done
-
-        git add .
     fi
 done