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In general, things that don't make sense in .sbt should be plugins, or treated as if they were plugins (for example the sonatype stuff could be its own .scala file and then configured/used in .sbt). javaversioncheck is now available as a plugin already: https://github.com/sbt/sbt-javaversioncheck
There is not a super compelling reason to do this though, no. .sbt files are the suggested way in new code but it isn't actively breaking anything to use the .scala file. So that's why it is tagged "would-be-nice cleanup" ;-)
I have a lot of issues I'd work on first.
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