I upgraded to sdfcli (java) 2025.1 and now I get a warning "Setting the <allroles> field to 'T' only selects all internal roles." for every single script in my project. Is there any way to confirm I just want internal roles so it can stop warning me?

You may have to update your SDF definitions to not include the 'allroles' element? I haven't run into this myself yet but perhaps try downloading one of your script SDF definitions anew - I'm guessing perhaps that will reflect changes with the 2025.1 release change to how the allroles checkbox works.

Excellent idea. Sadly, it's still called AllRoles when downloaded from a 2025.1 system, even though the field has been labelled "All Internal Roles" on-screen.