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Is there a way to specify an alternate scalastyle-config.xml under IntelliJ for test scope?

In build.sbt you can specify an alternate scalastyle config file for test scope using this:

(scalastyleConfig in Test) := baseDirectory.value / "scalastyle-test-config.xml"

This is useful when you want to loosen the checks in Test scope.

Unfortunately, IntelliJ ignores this setting and looks for the file in it's default location.

Is there a way to fix this?

This is currently not possible, the locations are hard-coded. I've created an issue for you: https://youtrack.jetbrains.com/issue/SCL-12086

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