The command line arguments are processed by the activator of the org.mitk.gui.qt.ext plugin. This means, if any plugin depends on this one, it will be loaded and it will process the command line arguments.
However, you might want to process the arguments yourself, e.g. because you want to introduce switches or options. The org.mitk.gui.qt.ext activator considers all the arguments as image files or MITK scenes, so it will print errors for any other options. If your app does not depend on org.mitk.gui.qt.ext then it can process the arguments in one of its own plugin, and everything is fine. However, this MITK plugin provides several useful classes, e.g. a workbench advisor that you won't be able to reuse.
My suggestion is to introduce a flag that can be set in the application launcher main cpp file, and can be read out from the plugin context in the activator. If the flag is set to 'false' then the MITK plugin does not process the arguments. If undefined, or set to any other value then yes.
Merge request follows.