Remove deprecated command line arguments

[oesteban]

We've been keeping some deprecated command-line arguments for some time - it is now the moment to drop them. These are:

• --ignore-aroma-denoising-errors
• --debug
• --output-space
• --template
• --template-resampling-grid
• --no-freesurfer
• --output-grid-reference (this is only present on the wrapper).

[mgxd]

Looking into this now - one question: is the docker wrapper meant to provide a very high level fmriprep call, while the fmriprep callable allows more fine-grain control? Or have we just not been synchronizing the two?

[effigies]

The Docker wrapper is meant to turn something that looks like an fMRIPrep invocation into a docker command. Any option that's valid in fMRIPrep should be valid in fMRIPrep docker. But it passes most things through, uninspected, only parsing options that will require it to mount a volume or some other manipulation of Docker.