[FIX] fixing some minor issues introduced recently

[yarikoptic]

Individual commits describe fixes better.
Follow up to #1392 .

closes #1423

• make sure that fixed references worked out as expected (checked on https://bids-specification--1411.org.readthedocs.build/en/1411/common-principles.html#filesystem-structure-filenames-richness-versus-distinctness -- all good)

[DimitriPapadopoulos]

The CI error is unrelated as far as I can see. Link https://nipy.org/nibabel/coordinate_systems.html does not exist any more, but that can be fixed in a separate PR.

Actually, it looks like the whole nipy.org domain is gone:

$ resolvectl query nipy.org
nipy.org: resolve call failed: 'nipy.org' not found
$ 

It's probably being renewed right now, whois output reads:

Updated Date: 2023-02-09T05:33:42Z
Creation Date: 2010-02-09T05:32:56Z
Registry Expiry Date: 2024-02-09T05:32:56Z

[effigies]

Looks like the nipy DNS is broken.

[Remi-Gau]

closes #1423