Fix discovery of project file for exclude

pick the outermost project file, so that if an excluded directory
is itself a scala-cli project then it is ignored.

fixes #3546

Author: bishabosha

modules/build/src/main/scala/scala/build/CrossSources.scala

@@ -190,9 +190,9 @@ object CrossSources {
 
     val flattenedInputs = inputs.flattened()
     val allExclude = { // supports only one exclude directive in one source file, which should be the project file.
-      val projectScalaFileOpt = flattenedInputs.collectFirst {
+      val projectScalaFileOpt = flattenedInputs.collect {
         case f: ProjectScalaFile => f
-      }
+      }.sortBy(_.subPath.segments.size).headOption
       val excludeFromProjectFile =
         value(preprocessSources(projectScalaFileOpt.toSeq))
           .flatMap(_.options).flatMap(_.internal.exclude)