After my genius idea to delete all stuff in this discussion, which only cause trouble and chaos, I figured out to do another attempt and post again. This is version 2 of the little app. The gui and commandline are streamlined into one app. The commandline options are flexible now and it supports a configuration file. Unfortunately in GUI mode only one patch file at a time is supported (but I think this is not a real issue and is a limitation in GUI only). And it can create output folders too. Updated the first post with all relevant information.
It started out so simple.