I think it get’s more and more confusing for you. Just as a background. You can compile ImageJ1 plugins in different ways:
The easiest way to compile ImageJ plugins is to use the ImageJ1 editor as @Herbie mentioned and simply compile the plugins. The plugin will run in ImageJ and in FIJI.
If you plan to write a more advanced plugin I highly recommend to use a IDE like you already use. This is why I sent you the IntelliJ plugin link from the imaging book which has a nice setup by default, too (to test and ship the plugin).
However you could also built a ImageJ1 plugin with Maven as described by @markkitt if you are familiar with maven or wan’t to use maven for the built process.
Maven is also the way to go if you want to create ImageJ2 API plugins (FIJI only).
Note (only to mention all compilation possibilities):
I also wrote an application (Bio7) to compile ImageJ1 plugins dynamically (in process with class reloading) using the Eclipse editor (also the regular ImageJ mechanism is supported). This is very nice for testing ImageJ plugins on the fly.