Fix clean task to delete managed sources located outside the target directory

main/src/main/scala/sbt/Defaults.scala

@@ -1965,18 +1965,7 @@ object Defaults extends BuildCommon with DefExtra {
   }
 
   /** Implements `cleanFiles` task. */
-  private[sbt] def cleanFilesTask: Initialize[Task[Vector[File]]] = {
-    import ScopeFilter.Make.*
-    val allConfigs = ScopeFilter(configurations = inAnyConfiguration)
-    Def.task {
-      val targetDir = target.value.toPath
-      val managedSrcDirs = managedSourceDirectories.?.all(allConfigs).value.flatten.flatten
-      val managedRscDirs = managedResourceDirectories.?.all(allConfigs).value.flatten.flatten
-      (managedSrcDirs ++ managedRscDirs)
-        .filter(d => !d.toPath.startsWith(targetDir))
-        .toVector
-    }
-  }
+  private[sbt] def cleanFilesTask: Initialize[Task[Vector[File]]] = Def.task { Vector.empty[File] }
 
   def runMainTask(
       classpath: Initialize[Task[Classpath]],

main/src/main/scala/sbt/internal/Clean.scala

@@ -107,7 +107,6 @@ private[sbt] object Clean {
           val excludeFilter = cleanFilter(scope).value
           val delete = cleanDelete(scope).value
           val targetDir = (scope / target).?.value.map(_.toPath)
-          val baseDir = (scope / baseDirectory).?.value.map(_.toPath)
 
           targetDir.withFilter(_ => full).foreach(deleteContents(_, excludeFilter, view, delete))
           (scope / cleanFiles).?.value.getOrElse(Nil).foreach { x =>
@@ -124,10 +123,8 @@ private[sbt] object Clean {
           val streamsGlobs =
             (streamsKey.toSeq ++ stampsKey)
               .map(k => manager(k).cacheDirectory.toPath.toGlob / **)
-          // Use baseDirectory instead of target so that file outputs outside the
-          // target directory but within the project root are also cleaned.
           ((scope / fileOutputs).value.filter { g =>
-            baseDir.fold(true)(g.base.startsWith)
+            targetDir.fold(true)(g.base.startsWith)
           } ++ streamsGlobs)
             .foreach { g =>
               val filter: Path => Boolean = { path =>

sbt-app/src/sbt-test/actions/clean-managed-outside-target/test

@@ -5,10 +5,3 @@ $ exists src_managed/demo/Test.scala
 > Compile / managedSourcePaths
 > Compile / managedSourcePaths / clean
 $ absent src_managed/demo/Test.scala
-
-# Test that clean also removes managed sources outside target
-> compile
-$ exists src_managed/demo/Test.scala
-
-> clean
-$ absent src_managed/demo/Test.scala