USE MAVEN https://github.com/games647/ScoreboardStats/blob/master/pom.xml

wtf man https://github.com/games647/ScoreboardStats/tree/master/sub/main/lib

You could at least provide instructions on how to compile your plugin. What's the point of you open sourcing it when nobody even have the slightest idea on how to compile it.

If you clone it from github, you shouldn't have a problem with it. Just choose the first pom for compiling and it will work.

Problem 1:

not all plugins have a maven repo

Problem 2:

I have to use NMS code on some parts so I need multiple versions of bukkit. But if I change only the version, maven might use only the newest version for compiling.

EDIT:

Look there: https://github.com/games647/ScoreboardStats/blob/master/sub/main/pom.xml
The Author of TagAPI found a way to solve this problem. I have tried it, but for me it doesn't worked.