Stencil Pull Theme Variations

[JakesObrien]

When running stencil pull I am unable to specify which config variables should be overridden.

I have a theme with four variations that are deployed to four stores (a variation for each), but this limitation means I am unable to pull the config changes to ensure they persist between deployments as by default stencil pull will update the core settings object which is then later overridden by the individual variation settings.

Is there a way around this or another approach that would allow me to update the individual variation settings?