Use sane way to delete files

Author: fido-node

src/main/scala/sbtprotoc/ProtocPlugin.scala

@@ -439,7 +439,15 @@ object ProtocPlugin extends AutoPlugin {
     val targetPaths = targets.map(_.outputPath).toSet
 
     if (deleteTargetDirectory) {
-      targetPaths.foreach(IO.delete)
+
+      targetPaths.foreach(targetPath => {
+        def fileList = (targetPath ** "*.scala").get().toSet[File]
+        fileList.foreach { f =>
+          if (IO.read(f).startsWith("// Generated by the Scala Plugin for the Protocol Buffer Compiler.")) {
+            IO.delete(f)
+          }
+        }
+      })
     }
 
     targets