Merge cohort entity into space entity in derivatives

[tsalo]

Closes #501.

Changes proposed:

• Combine space and cohort entities in the form space-<space>+<cohort> in derivatives. This matches how transforms are written out, and shouldn't impact potential derivatives with the template entity (which can have the cohort entity in the filename).

[codecov]

Codecov Report

❌ Patch coverage is 10.00000% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 57.14%. Comparing base (23c6af6) to head (9996fd4).
⚠️ Report is 10 commits behind head on master.

Files with missing lines	Patch %	Lines
nibabies/utils/bids.py	12.50%	7 Missing ⚠️
nibabies/workflows/anatomical/outputs.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #524      +/-   ##
==========================================
- Coverage   57.21%   57.14%   -0.07%     
==========================================
  Files          72       72              
  Lines        6977     6987      +10     
  Branches      860      863       +3     
==========================================
+ Hits         3992     3993       +1     
- Misses       2763     2772       +9     
  Partials      222      222              

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[mgxd]

we should bump the pyproject.toml to build off smriprep master, I feel like a lot of this was covered in your smriprep PR.

btw, error was buried in CI (and not being detected..)

260216-19:15:51,604 nipype.workflow ERROR:
         Node combine_space.a0 failed to run on host f2d3c5784311.
260216-19:15:51,604 nipype.workflow ERROR:
         Saving crash info to /out/sub-01/ses-1mo/log/20260216-191536_2073aff4-1f47-44ef-b8e6-dcb171c8ba2c/crash-20260216-191551-UID1001-combine_space.a0-a91c9796-7a77-4a05-8709-35716e403122.txt
Traceback (most recent call last):
  File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/pipeline/plugins/multiproc.py", line 389, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 733, in _run_command
    result.outputs = clean_working_directory(
                     ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.12/site-packages/nipype/pipeline/engine/utils.py", line 1445, in clean_working_directory
    output_files.extend(walk_outputs(outputdict[output]))
                                     ~~~~~~~~~~^^^^^^^^
KeyError: 'space'

[mgxd]

LGTM, thanks!