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I'm not sure how capable Migration Manager is about finding binary changes with Scala.js artifacts or not, but adding a setting for it at least allows ScalaCheck to publish Scala.js artifacts rather than MiMa needlessly failing.
I tested this, by running the following locally:
Starting sbt with
env SCALAJS_VERSION=1.0.0-M8 sbt
.This should help with publishing 2.12 and 2.13 artifacts for Scala.js 1.0.0-M8 per #474.