Refactor CuBIDS to support file collections

[tsalo]

Closes .

Changes proposed in this pull request

• Add file collection entities (echo, mt, flip, part, and inv) to NON_KEY_ENTITIES.
• Replace "modality" with "datatype" when applicable.
• Draft function to resolve BIDS URIs in IntendedFor definitions (resolve_bids_uri).
• Use BIDSLayout when possible, instead of string manipulation and globbing.

Documentation that should be reviewed

[codecov-commenter]

Codecov Report

Attention: 48 lines in your changes are missing coverage. Please review.

Comparison is base (39770dc) 62.13% compared to head (c81bd2e) 59.65%.
Report is 2 commits behind head on main.

Files	Patch %	Lines
cubids/cubids.py	79.11%	33 Missing ⚠️
cubids/utils.py	6.66%	14 Missing ⚠️
cubids/workflows.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #308      +/-   ##
==========================================
- Coverage   62.13%   59.65%   -2.48%     
==========================================
  Files           9        9              
  Lines        1582     1527      -55     
==========================================
- Hits          983      911      -72     
- Misses        599      616      +17     

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

[tsalo]

The BOLD filenames seem to be working correctly, but the associated files, including fmaps, aren't being updated.

[tsalo]

Closing in favor of #403 and #407.