As per previous post the command syntax change branch has now been merged, if you get your xia2 from git your next git pull will be a big one and you may find e.g. -resolution / -atom etc don't work any more... The functionality is still there however, you just need to use atom=Se (say) or anomalous=true, d_min=1.6... full documentation will follow of the changes.
The pipeline options -3d. etc remain however are now deprecated but still work, you will get a note saying "please use pipeline=3d"
Please if you find any bugs as a side-effect of this contact email@example.com or add an issue at