Describe the bug
Our installation has an institution logo image at this location:

/usr/local/submitty/site/public/img/<INSTITUTION_LOGO>.png

It is displayed as part of the SAML login screen, see also:
https://submitty.org/sysadmin/configuration/saml_authentication

but when we run
/usr/local/submitty/.setup/INSTALL_SUBMITTY.sh clean

That file is deleted and not restored.

Expected behavior
Like the files located in /usr/local/submitty/config, we should redesign how clean works and/or where these files are stored or how/where they are copied from on an install so we don't lose/have to repair the installation.

EDITED TO ADD:

I believe the

/usr/local/submitty/config/footer_links.json

file is also lost on clean. It should be preserved if it exists.