Minecraft NEW Launcher doesn't allow ANY changes in the JAR files

So since I updated to the new launcher (that doesn't require java) and if I decide to change ANYTHING in the JAR files of the versions, and I open MC, it downloads the version and undos ALL my changes... This can be awful ESPECIALLY with beta as you need to change the files in order to add modloaders... I've only tried with windows 10 and it does that with the 2.0.0 and future versions of the launcher!