Include optional submodules and staged diffs in fleximod_test.yaml

[samsrabin]

Description of changes

CTSM ran into an issue that wasn't caught until -o was added here and the status check was changed to include staged diffs.

Specific notes

Contributors other than yourself, if any: None

Fixes: None

User interface changes?: No

Testing performed (automated tests and/or manual tests): GitHub workflow.