For effects processing, you could create instances of your effects and then process it in chunks, similar to how I'm doing the FFT. 

Finally, for saving to disk, you'll have to get a bit trickier. You will need to write a class that implements the Recordable interface and then pass an instance of that to the createRecorder method of Minim. The AudioRecorder will set itself as an AudioListener to your Recordable instance and when you are ready to save samples to disk, you simply call the samples method of the listener. You could either choose to do this in chunks, like with FFT and effects processing, or you could choose to write the entire buffer at once. Whichever you choose, you simply need to make sure that the value returned by the bufferSize method of your Recordable instance is the same as the length of the float array you pass to the samples method.

All of this makes me think I should just write a saveFile method for Minim.

  You will need to write a class that implements the Recordable interface and then pass an instance of that to the createRecorder method of Minim.

Okay, AudioSample implements Recordable, right? So we can use this?

The AudioRecorder will set itself as an AudioListener to your Recordable instance

Here i already get lost, probably i didn't get the concept of the AudioListener. How can AudioRecorder "set itself as an AudioListener", although AudioRecorder does not implement AudioListener?

and when you are ready to save samples to disk, you simply call the samples method of the listener.

How can i do this? I don't know how to adress this listener...

Forgive me my stupidity!

Perhaps you find the time to write an example which dies what you described?