I would like to know how to make a configuration file for my velocity plugin since there is not tutorial or explication in the documentation
If you are still searching for a anwser.
Have a look on how I implemented it in my plugin. https://github.com/strifel/VBans/blob/master/src/main/java/de/strifel/vbans/VBans.java (loadConfig Method).
I dont know if this is best practice, but I think I saw this very similar in another plugin.