tests: fix existing tests when add an ignore=all submodule

There are tests that rely on "git add <submodule>" to add updates in the
parent repository. A new option --include-ignored-submodules is introduced
as it is now needed with this enhancement.

Updated tests:
- t1013-read-tree-submodule.sh ( fixed in: t/lib-submodule-update.sh )
- t2013-checkout-submodule.sh ( fixed in: t/lib-submodule-update.sh )
- t7406-submodule-update.sh
- t7508-status.sh

Signed-off-by: Claus Schneider(Eficode) <claus.schneider@eficode.com>

Author: bicschneider

t/lib-submodule-update.sh

@@ -95,14 +95,14 @@ create_lib_submodule_repo () {
 			git commit -m "modified file2 and added file3" &&
 			git push origin modifications
 		) &&
-		git add sub1 &&
+		git add --include-ignored-submodules sub1 &&
 		git commit -m "Modify sub1" &&
 
 		git checkout -b add_nested_sub modify_sub1 &&
 		git -C sub1 checkout -b "add_nested_sub" &&
 		git -C sub1 submodule add --branch no_submodule ../submodule_update_sub2 sub2 &&
 		git -C sub1 commit -a -m "add a nested submodule" &&
-		git add sub1 &&
+		git add --include-ignored-submodules sub1 &&
 		git commit -a -m "update submodule, that updates a nested submodule" &&
 		git checkout -b modify_sub1_recursively &&
 		git -C sub1 checkout -b modify_sub1_recursively &&
@@ -112,7 +112,7 @@ create_lib_submodule_repo () {
 		git -C sub1/sub2 commit -m "make a change in nested sub" &&
 		git -C sub1 add sub2 &&
 		git -C sub1 commit -m "update nested sub" &&
-		git add sub1 &&
+		git add --include-ignored-submodules sub1 &&
 		git commit -m "update sub1, that updates nested sub" &&
 		git -C sub1 push origin modify_sub1_recursively &&
 		git -C sub1/sub2 push origin modify_sub1_recursively &&

t/t7508-status.sh

@@ -1565,7 +1565,7 @@ test_expect_success 'git commit will commit a staged but ignored submodule' '
 
 test_expect_success 'git commit --dry-run will show a staged but ignored submodule' '
 	git reset HEAD^ &&
-	git add sm &&
+	git add --include-ignored-submodules sm &&
 	cat >expect << EOF &&
 On branch main
 Your branch and '\''upstream'\'' have diverged,