This is not not perfect yet, but seems better to me, the actual patch is:

diff --git a/src/main/scala/com/typesafe/sbt/SbtScalariform.scala b/src/main/scala/com/typesafe/sbt/SbtScalariform.scala
index 8d46caa..63e51b4 100644
--- a/src/main/scala/com/typesafe/sbt/SbtScalariform.scala
+++ b/src/main/scala/com/typesafe/sbt/SbtScalariform.scala
@@ -84,7 +84,7 @@ object SbtScalariform extends AutoPlugin {

   def configScalariformSettings: Seq[Setting[_]] =
     List(
-      (sourceDirectories in Global in scalariformFormat) := List(scalaSource.value),
+      (sourceDirectories in Global in scalariformFormat) := unmanagedSourceDirectories.value,
       scalariformFormat := Scalariform(
         scalariformPreferences.value,
         (sourceDirectories in scalariformFormat).value.toList,