I found it easiest to create a simple batch file to run it, however it won't work on the server files in the dedicated server folder.   It works fine in my working folder for map generation so it was just a case of making a temp folder to work on any maps that lack flowers.   flower.bat java -jar flowerspawner.jar %1 %2 %3 All you need to do is open a command prompt and type  flower top_layer.map top_layer_new.map 25 Just because I'm a lazy git and prefer to make life as easy