Align CLI arguments with reader APIs for full parameter consistency#321

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Copilot wants to merge 3 commits intomainfrom

copilot/fix-343cb2c5-5474-4b02-b011-67557f9c973a

Commits on Sep 5, 2025

Initial plan
Copilot
committed
Fix CLI mismatches: add missing parameters for seqfish, visium, visium_hd, and macsima

Copilot
and
LucaMarconato
committed
Add complete CLI/API alignment: JSON kwargs parameters for all readers

Copilot
and
LucaMarconato
committed