diff-lib: honor override_submodule_config flag bit

diff-lib: honor override_submodule_config flag bit

When `diff.ignoreSubmodules = all` is set and submodule commits are
manually staged (e.g. via `git-update-index`), `git-commit` should
record the commit  with updated submodules.

`index_differs_from` is called from `prepare_to_commit` with flags set to
`override_submodule_config = 1`. `index_differs_from` then merges the
default diff flags and passed flags.

When `diff.ignoreSubmodules` is set to "all", `flags` ends up having
both `override_submodule_config` and `ignore_submodules` set to 1. This
results in `git-commit` ignoring staged commits.

This patch restores original `flags.ignore_submodule` if
`flags.override_submodule_config` is set.

Signed-off-by: Josip Sokcevic <sokcevic@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>