DOC: Altered CLI option grouping

[Lestropie]

Back when I commenced some work on #2207 (from which I'll need to familiarise myself with #2913), I started by looking at the CLI and thinking about what the right interface would be for such a capability (see eg. #2805, #2806). I immediately found some command-line options that really felt as though they were in the wrong place. So here I've separated out the set of CLI changes that I'd generated in the course of that little experiment.

The git diff is quite unclean, so I've produced the set of options that would be moved and their corresponding old and new option groups.

Option	Old option group	New option group
--anat-only	Options to handle performance	Options for performing only a subset of the workflow
--boilerplate-only	Options to handle performance	Options for performing only a subset of the workflow
--md-only-boilerplate	Options to handle performance	Options for modulating outputs
--cifti-output	Surface preprocessing options	Workflow configuration
--error-on-aroma-warnings	Options to handle performance	Specific options for running ICA_AROMA
--verbose	Options to handle performance	Other options
--me-output-echos	Workflow configuration	Options for modulating outputs
--medial-surface-nan	Workflow configuration	Options for modulating outputs
--no-submm-recon	Surface preprocessing options	Specific options for FreeSurfer processing
--output-layout	Other options	Options for modulating outputs
--sloppy	Other options	Options to handle performance
--track-carbon	Other options	Options for carbon tracking
--country-code	Other options	Options for carbon tracking

New option groups:

• "Options for performing only a subset of the workflow"
• "Options for modulating outputs"
• "Options for carbon tracking"

Deleted option groups:

• "Surface preprocessing options"

In particular, "Options for performing only a subset of the workflow" is what I was looking for in the context of #2207, where I had initially added command-line options "--fmri_withhold" and "--fmri_regenerate" (the naming of such options should perhaps be discussed in #2913).

Open to modification of proposed changes, or indeed addition of other changes (since this would be a good opportunity to review placement of the complete set of command-line options). For instance I'm currently looking at [ --output-spaces, --cifti-output, --me-output-echos ] as a candidate option group.

[welcome]

Thanks for opening this pull request! It looks like this is your first time contributing to fMRIPrep. 😄
We invite you to list yourself as an fMRIPrep contributor. To learn more about what that entails and how we credit our contributors, please check out the contributing guidelines. If your name is not already on the list, please insert it, in alphabetical order, into the contributors.json file. Example:

   "name": "Contributor, New FMRIPrep",
   "affiliation": "Department of fMRI prep'ing, Open Science Made-Up University",
   "orcid": "<your id>"
}, ```

Of course, if you want to opt-out this time there is no problem at all with adding your name later. You will be always welcome to add it in the future whenever you feel it should be listed.

[mgxd]

Thank you for the contribution @Lestropie! I agree - our CLI grouping has gotten rather large and disorganized, so a restructuring is much needed. I've had a quick look and the changes look sensible to me, just left a few comments

If you would like, feel free to add yourself to the contributors file

[Lestropie]

Good catches @mgxd; should all be resolved.