Add --session-id parameter and support longitudinal output structure

[tsalo]

Closes nipreps/smriprep#429. I've only just started on this, and it won't deal with lingering longitudinal issues, such as:

1. Writing out session-level HTML reports to the subject's session folder.
   • Not sure how I feel about this one TBH.
2. Writing out session-level figures to the subject's session folder (see HTML report folder structure does not work for ongoing longitudinal out of the box nibabies#350).
3. Running FreeSurfer on a session-wise basis (see Alter FreeSurfer subjects to include session labels nibabies#288).

Changes proposed in this pull request

• Add --session-id command line parameter.
• Copy over longitudinal organization code from Nibabies.
  • In order to collect session-wise anatomical derivatives, we need to either add a session_id parameter to smriprep.utils.bids.collect_derivatives() or adopt Nibabies' nibabies.utils.bids.Derivatives class. Which is better?

[codecov]

Codecov Report

Attention: Patch coverage is 61.11111% with 14 lines in your changes are missing coverage. Please review.

Project coverage is 66.50%. Comparing base (8eb8215) to head (1672988).

Files	Patch %	Lines
fmriprep/workflows/base.py	18.18%	9 Missing ⚠️
fmriprep/cli/parser.py	88.23%	2 Missing ⚠️
fmriprep/cli/workflow.py	0.00%	2 Missing ⚠️
fmriprep/config.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    nipreps/fmriprep#3265      +/-   ##
==========================================
- Coverage   73.62%   66.50%   -7.13%     
==========================================
  Files          56       56              
  Lines        4243     4266      +23     
==========================================
- Hits         3124     2837     -287     
- Misses       1119     1429     +310     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.