My recollection is that this was discussed earlier, but one of the problems is the eclipse will “partially compile” a class that contains errors. This is useful within eclipse when running unit tests for example. However, these partially compiled class files can be a real pain as gradle javaCompile can succeed even though there are compile errors. In other words a .class file generated by the partial compile by eclipse hides the fact that gradle really needs to recompile that java file. Can lead to some really hard to figure out bugs and means that you have to do a ‘gradle clean’ often to make sure your compile really did succeed.
What the default eclipse output directory should be called is I guess a separate question, but it shouldn’t be the same as gradle’s output directory.
Philip