DOC: Update description of output layout, add discussion of legacy mode

[effigies]

Closes #2645.

[codecov-commenter]

Codecov Report

Merging #2646 (b460938) into master (67d8dfc) will increase coverage by 0.55%.
The diff coverage is 30.52%.

@@            Coverage Diff             @@
##           master    #2646      +/-   ##
==========================================
+ Coverage   44.90%   45.46%   +0.55%     
==========================================
  Files          41       41              
  Lines        3089     3161      +72     
==========================================
+ Hits         1387     1437      +50     
- Misses       1702     1724      +22     

Impacted Files	Coverage Δ
fmriprep/cli/workflow.py	3.29% <ø> (ø)
fmriprep/workflows/base.py	9.48% <0.00%> (-1.17%)	⬇️
fmriprep/workflows/bold/t2s.py	43.75% <0.00%> (ø)
fmriprep/workflows/bold/resampling.py	10.48% <4.08%> (ø)
fmriprep/workflows/bold/base.py	17.16% <5.08%> (-0.62%)	⬇️
fmriprep/workflows/bold/outputs.py	25.20% <53.84%> (+3.38%)	⬆️
fmriprep/cli/parser.py	82.19% <100.00%> (+4.83%)	⬆️
fmriprep/cli/tests/test_parser.py	100.00% <100.00%> (ø)
fmriprep/config.py	79.12% <100.00%> (+0.06%)	⬆️
fmriprep/interfaces/multiecho.py	79.31% <100.00%> (ø)
... and 2 more

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