[Robert Withers]"I don't know what the first one means, I don't think I need a “java” command-line tool cause I never did before."
Apparently something you are using does. Apple stopped shipping Java some time ago so I'm assuming whatever OS X version you had came with Java and now El Capitan does not.
[Robert Withers]"I downloaded and installed a java program to see if it would help but it didn't. How can I stop this from appearing?"
Go to System Preferences | Users & Groups | Login Items and check the items in the list to try and see which one needs Java. There is no way to disable them to find out except to remove them which may not be desirable. Then contact the manufacturer to find out which Java they require. Installing the latest Java 8 might not help you if the app you are running requires Java 6 (which is the last version Apple shipped before stopping)