These versions are also called "stages" and the command to pick on is magit-checkout-stage. You can invoke that using M-x of course, but you can also just press k (magit-discard) on the conflicting file to discard the other stages. (But be aware that this prompts you for which side to keep, not which side to discard.)
Choose your tool
If you have installed ag and not rg then ag will be used according to the documentation string in your dotfile you can see that Spacemacs tries the search tool in this order first rg, then ag, pt, ack and finally grep.
Hack your tool
One solution is to use the options of the tool you are using in your case for ag:
create a .agignore ignore ...