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After looking for a while I found this seemingly decent course https://www.udemy.com/java-tutorial/ which appears to be free and should be a good way to learn the basics of Java.
If your daring you can skip that part (and hop to land on your feet) and start going directly into bukkit/spigot. This series has LOAAADS of helpful videos on how to do stuff using bukkit/spigot. (Please not that in the video he will be using bukkit, you will be using spigot)
Ah, I just found something awesome out a while ago. Codecademy now teaches Java and is developing lessons, so keep that in mind when looking for websites to learn to program.
Sorry for the Necro Post, but a lot can change in a few months.