fix add to skip submodules configured as ignored

If submodules are configured as ignore=all they are not shown by status.
Lets also ignore them when adding files to the index. This avoids that
users accidentially add ignored submodules with: git add .

We achieve this by reading the submodule config and thus correctly
initializing the infrastructure to take the ignore decision.
DRAFT: use parse_options api in diff for commandline switches
Merge remote-tracking branch 'hvoigt/hv/fix_submodule_index_diff_ignore' into hv/fix_submodule_index_diff_ignore