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

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

@@ -1965,7 +1965,18 @@ object Defaults extends BuildCommon with DefExtra {
   }
 
   /** Implements `cleanFiles` task. */
-  private[sbt] def cleanFilesTask: Initialize[Task[Vector[File]]] = Def.task { Vector.empty[File] }
+  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
+    }
+  }
 
   def runMainTask(
       classpath: Initialize[Task[Classpath]],

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

@@ -107,6 +107,7 @@ 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 =>
@@ -123,8 +124,10 @@ 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 =>
-            targetDir.fold(true)(g.base.startsWith)
+            baseDir.fold(true)(g.base.startsWith)
           } ++ streamsGlobs)
             .foreach { g =>
               val filter: Path => Boolean = { path =>

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

@@ -1,6 +1,14 @@
+# Test that managedSourcePaths / clean removes managed sources outside target
 > compile
 $ 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