Revisit warning message for unsupported BIDS suffixes in `bids2tsv`

[alyssadai]

Since:

1. bids2table includes essentially every file suffix encountered in a BIDS dataset in the output suffix column, and
2. our bids2tsv command looks at the difference between the bid2table-generated suffix column and the Neurobagel-supported list of image file suffixes to identify "unrecognized" suffixes,

our warnings about unrecognized suffixes currently include non-imaging-related suffixes such as sessions and scans:

$ bagel bids2tsv -b tests/bids-examples/synthetic -f
[2025-11-26 13:32:34] INFO     Input BIDS directory:  D:\neurobagel\bagelbids\tests\bids-examples\synthetic
[2025-11-26 13:32:34] INFO     BIDS validation passed.
[2025-11-26 13:32:34] WARNING  Image file suffixes unsupported by Neurobagel were found in the BIDS directory: ['sessions', 'scans', 'beh', 'physio', 'stim']. These will be ignored. Supported BIDS suffixes: ['dwi', 'T1w',    
                               'T2w', 'bold', 'asl', 'eeg', 'meg', 'pet'].
[2025-11-26 13:32:34] INFO     Saved output to:  D:\neurobagel\bagelbids\bids.tsv

To avoid unnecessarily verbose warnings (and raising alarm about irrelevant suffixes), we should see if we can:

• include only unrecognized imaging suffixes in the warning (maybe there is an importable version of this list https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html ?)
  • note: https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/suffixes.yaml is not restrictive enough
  • can use bidsschematools to access these suffix lists
• first check: against all BIDS file suffixes (from suffixes.yaml) and warn about any ones unrecognized (e.g., typos or custom)
• second check: filter for BIDS raw file suffixes (https://github.com/bids-standard/bids-specification/tree/master/src/schema/rules/files/raw) and then check against Neurobagel-supported list; warn about unsupported suffixes

[alyssadai]

Types of suffixes we have:
A. Neurobagel supported BIDS raw data suffixes
B. All BIDS file suffixes (not just raw data, but also sessions, scans, etc. - this was the motivation behind the original issue)
C. All BIDS raw data suffixes

For a given list of suffixes (S) detected in an input BIDS directory, we need to:

1. ERROR if S and A have no suffixes in common
2. WARN if S contains suffixes not found in B
3. WARN if S contains suffixes FOUND in C but not in A

AND

• the warning messages for 2 and 3 should be different
• 1 should happen first if the condition is met

If all suffixes are unsupported by Neurobagel,
Implementation 1:

• Warn that subset X is completely BIDS invalid (and then remove subset X for remaining comparisons)
• Warn that subset Y is BIDS valid but not Neurobagel valid (and then remove subset Y from "")
• Are there any suffixes left? if no, error about "no valid suffixes left"

Implementation 2:

• Error that there are no suffixes valid for Neurobagel, and list all the input suffixes