Is there a way to disable all together the confirmation check-in changes?
One answer
There's a preference to set the default option (yes, no, or cancel). See the menu: Window > Preferences > Team > Jazz Source Control > Notification Dialogs > Default action when delivering while there are unresolved changes.
Your other option that I think makes the most sense is to add those unresolved files to the ignore list.
Your other option that I think makes the most sense is to add those unresolved files to the ignore list.