I saw a nice course being offered via Duke University on Arrays, Lists and Structured Data. However, they utilize custom libraries created by Duke Univ. Another course through Princeton had the same nonsense. As someone who knows/is learning standard Java API, I can't help but feel that this would cripple me as I move into a junior level role in the real world, as some of programming is, after all, familiarity/muscle-memory and knowing your libraries. Thoughts?
Find out what the custom libraries are. If they are simply input utilities, they may not be too bad. I personally don't like the Princeton libraries because they try to be too comprehensive, but others may differ.
Someone posted their assignment answers on github. (I recommend you not go through them since you are thinking of taking the class. From this, Iw as able to learn that they are using some standard libraries like StringBuilder, HashMap and HashSet. They are also use some custom libraries for File IO, Network IO and graphics type stuff. They also use the Apache Commons CSV library - a well used open source libraries.
I think this is fine. The core of what they are trying to teach does use standard Java. And learning to work with libraries is an important skill too. So I think they are offering a good mix.