Hi Xavier, I think it's fine to support both modes. However i'm concerned with existing libraries that cannot be extracted due to case sensitivity, and a global flag can damage these jars. Moreover developers may not be aware of that flag and won't understand why their build fails. If i may, i would suggest to go by the origin, i.e. if a library comes as a jar, leave it as a jar, and have the transformation generate its output as a jar. If the origin are class files (like in the Project itself), then leave extracted. This way 3rd party jars will not get damaged, and we will also provide good support for incremental builds, which usually involve only changing of class files in the Project. What do you think?
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