RF/DOC: Parser defaults

[mgxd]

Renders fmriprep proper defaults in the sphinx documentation.

A few drive-by changes:

• --no-submm-recon and --no-msm are now argparse.BooleanOptionalActions
• --work-dir default is set during argument parsing (to avoid rendering an arbitrary path when docs are built)

[codecov]

Codecov Report

❌ Patch coverage is 80.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.49%. Comparing base (2263b64) to head (a38e10f).
⚠️ Report is 5 commits behind head on master.

Files with missing lines	Patch %	Lines
fmriprep/cli/parser.py	50.00%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #3487   +/-   ##
=======================================
  Coverage   73.49%   73.49%           
=======================================
  Files          60       60           
  Lines        4572     4580    +8     
  Branches      584      585    +1     
=======================================
+ Hits         3360     3366    +6     
- Misses       1084     1085    +1     
- Partials      128      129    +1     

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