DEV Upgrade - Core File/Folder Structures

What are the core file/folder structures that could change/overwrite during DEV new releases or updates? especially, livewhale/integrations/saml/idp-cert.pem? Does it get overwritten for any new releases on DEV? anyway to exclude that to change?

Unless otherwise noted in the release notes, LiveWhale upgrades only change/overwrite files inside of:
/livewhale/core/ (except for config.php which contains site credentials)
/public_html/livewhale/

Anything you configure within /livewhale/client/ or /livewhale/integrations/ shouldn’t ever be touched by the upgrade process, including the SAML certificate you mentioned (idp-cert.pem).