diff --git a/main/src/main/scala/sbt/Defaults.scala b/main/src/main/scala/sbt/Defaults.scala
index 28fa89f30..9b5ed9bcc 100644
--- a/main/src/main/scala/sbt/Defaults.scala
+++ b/main/src/main/scala/sbt/Defaults.scala
@@ -541,10 +541,13 @@ object Defaults extends BuildCommon {
     scalaSource := sourceDirectory.value / "scala",
     javaSource := sourceDirectory.value / "java",
     unmanagedSourceDirectories := {
+      val isDotty = ScalaInstance.isDotty(scalaVersion.value)
+      val epochVersion = if (isDotty) "3" else "2"
       makeCrossSources(
         scalaSource.value,
         javaSource.value,
         scalaBinaryVersion.value,
+        epochVersion,
         crossPaths.value
       ) ++
         makePluginCrossSources(
@@ -671,6 +674,24 @@ object Defaults extends BuildCommon {
     )
   )
 
+  def makeCrossSources(
+      scalaSrcDir: File,
+      javaSrcDir: File,
+      sv: String,
+      epochVersion: String,
+      cross: Boolean
+  ): Seq[File] = {
+    if (cross)
+      Seq(
+        scalaSrcDir,
+        scalaSrcDir.getParentFile / s"${scalaSrcDir.name}-$sv",
+        scalaSrcDir.getParentFile / s"${scalaSrcDir.name}-$epochVersion",
+        javaSrcDir,
+      )
+    else
+      Seq(scalaSrcDir, javaSrcDir)
+  }
+
   def makeCrossSources(
       scalaSrcDir: File,
       javaSrcDir: File,
diff --git a/sbt/src/sbt-test/actions/cross-strict-aggregation/core/A.scala b/sbt/src/sbt-test/actions/cross-strict-aggregation/core/src/main/scala-2/A.scala
similarity index 100%
rename from sbt/src/sbt-test/actions/cross-strict-aggregation/core/A.scala
rename to sbt/src/sbt-test/actions/cross-strict-aggregation/core/src/main/scala-2/A.scala
diff --git a/sbt/src/sbt-test/plugins/dotty/src/main/scala/Main.scala b/sbt/src/sbt-test/plugins/dotty/src/main/scala-3/Main.scala
similarity index 100%
rename from sbt/src/sbt-test/plugins/dotty/src/main/scala/Main.scala
rename to sbt/src/sbt-test/plugins/dotty/src/main/scala-3/Main.scala
diff --git a/sbt/src/sbt-test/plugins/dotty/src/main/scala/TraitParams.scala b/sbt/src/sbt-test/plugins/dotty/src/main/scala-3/TraitParams.scala
similarity index 100%
rename from sbt/src/sbt-test/plugins/dotty/src/main/scala/TraitParams.scala
rename to sbt/src/sbt-test/plugins/dotty/src/main/scala-3/TraitParams.scala