Update subject segmentation outputs

[htwangtw]

Closes #143.

• Make the working dir output follow the atlas etc convention
• --working-dir -> --atlases-dir
• Drop space, res, atlas in the outputs and replace with seg
• Schaefer20187Networks -> Schaefer2018 for simplicity.

It would be useful if someone (also know as Chris or Oscar) can have a look at the output layout in the documentation (docs/source/outputs.md) to make sure it makes sense. I can make sure I change the code accordingly.

To-do

• Depreciation warning of CLI

[codecov]

Codecov Report

Attention: Patch coverage is 96.96970% with 3 lines in your changes missing coverage. Please review.

Project coverage is 93.20%. Comparing base (ced47b3) to head (18c1384).
Report is 14 commits behind head on main.

Files	Patch %	Lines
giga_connectome/postprocess.py	83.33%	1 Missing ⚠️
giga_connectome/run.py	92.30%	1 Missing ⚠️
giga_connectome/utils.py	93.75%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #146      +/-   ##
==========================================
+ Coverage   92.58%   93.20%   +0.62%     
==========================================
  Files          18       18              
  Lines         715      751      +36     
==========================================
+ Hits          662      700      +38     
+ Misses         53       51       -2     

Files	Coverage Δ
giga_connectome/atlas.py	90.54% <100.00%> (+3.58%)	⬆️
giga_connectome/mask.py	94.50% <100.00%> (+0.56%)	⬆️
giga_connectome/tests/test_atlas.py	100.00% <100.00%> (ø)
giga_connectome/tests/test_cli.py	97.87% <100.00%> (+0.14%)	⬆️
giga_connectome/tests/test_mask.py	100.00% <100.00%> (ø)
giga_connectome/tests/test_utils.py	100.00% <100.00%> (ø)
giga_connectome/workflow.py	89.36% <100.00%> (ø)
giga_connectome/postprocess.py	89.18% <83.33%> (+0.14%)	⬆️
giga_connectome/run.py	95.34% <92.30%> (-1.32%)	⬇️
giga_connectome/utils.py	88.57% <93.75%> (+0.33%)	⬆️