eclass/git-r3: Sync with Gentoo

It's from Gentoo commit 838b52b4a3e44aaa2b86db7c68803d0018cfba98.

sdk_container/src/third_party/portage-stable/eclass/git-r3.eclass

@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 # @ECLASS: git-r3.eclass
@@ -429,6 +429,7 @@ _git-r3_set_submodules() {
 
 		l=${l#submodule.}
 		local subname=${l%%.url=*}
+		local is_manually_specified=
 
 		# filter out on EGIT_SUBMODULES
 		if declare -p EGIT_SUBMODULES &>/dev/null; then
@@ -449,13 +450,14 @@ _git-r3_set_submodules() {
 				continue
 			else
 				einfo "Using submodule ${parent_path}${subname}"
+				is_manually_specified=1
 			fi
 		fi
 
 		# skip modules that have 'update = none', bug #487262.
 		local upd=$(echo "${data}" | git config -f /dev/fd/0 \
 			submodule."${subname}".update)
-		[[ ${upd} == none ]] && continue
+		[[ ${upd} == none && ! ${is_manually_specified} ]] && continue
 
 		# https://github.com/git/git/blob/master/refs.c#L31
 		# we are more restrictive than git itself but that should not
@@ -813,13 +815,17 @@ git-r3_fetch() {
 
 		if [[ ${EGIT_LFS} ]]; then
 			# Fetch the LFS files from the current ref (if any)
-			local lfs_fetch_command=( git lfs fetch "${r}" )
+			local lfs_fetch_command=( git lfs fetch "${r}" "${remote_ref}" )
 
 			case "${EGIT_LFS_CLONE_TYPE}" in
 				shallow)
-					lfs_fetch_command+=(
-						--prune
-					)
+					if [[ -d ${GIT_DIR}/lfs/objects ]] && ! rmdir "${GIT_DIR}"/lfs/objects 2> /dev/null; then
+						# Only prune if the lfs directory is not empty.
+						# The prune command can take a very long time to resolve even if there are no lfs objects.
+						lfs_fetch_command+=(
+							--prune
+						)
+					fi
 					;;
 				single)
 					;;