[2.x] fix: Allow cleanFileOutputTask to delete files outside target directory

**Problem**
When sourceManaged or resourceManaged is set to a path outside the target
directory, neither clean nor managedSourcePaths/clean removes the generated
files. The cleanFileOutputTask has a hard guard that skips any file not
inside the target directory, even though these files are tracked via the
previous mechanism and were produced by the task itself.

**Solution**
Replace the targetDir guard in cleanFileOutputTask with a baseDirectory
guard. Files tracked by previous are task-produced outputs that are safe
to delete as long as they are within the project root. The
cleanKeepFiles/cleanKeepGlobs filter still applies for user-specified
exclusions.

Fixes #6895

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

@@ -167,10 +167,9 @@ private[sbt] object Clean {
       })
       .flatMapTask { case scope =>
         Def.task {
-          val targetDir = (scope / target).value.toPath
+          val baseDir = (scope / baseDirectory).value.toPath
           val filter = cleanFilter(scope).value
-          // We do not want to inadvertently delete files that are not in the target directory.
-          val excludeFilter: Path => Boolean = path => !path.startsWith(targetDir) || filter(path)
+          val excludeFilter: Path => Boolean = path => !path.startsWith(baseDir) || filter(path)
           val delete = cleanDelete(scope).value
           val st = (scope / streams).value
           taskKey.previous.foreach(_.toSeqPath.foreach(p => if (!excludeFilter(p)) delete(p)))

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

@@ -0,0 +1,8 @@
+name := "clean-managed-outside-target"
+scalaVersion := "3.3.1"
+Compile / sourceManaged := baseDirectory.value / "src_managed"
+Compile / sourceGenerators += Def.task {
+  val file = (Compile / sourceManaged).value / "demo" / "Test.scala"
+  IO.write(file, """object Test extends App { println("Hi") }""")
+  Seq(file)
+}.taskValue

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

@@ -0,0 +1,6 @@
+> compile
+$ exists src_managed/demo/Test.scala
+
+> Compile / managedSourcePaths
+> Compile / managedSourcePaths / clean
+$ absent src_managed/demo/Test.scala