Summary
Refined-X loads collections from a configurable contentRoot so a vault or monorepo publish folder can stay outside the site package.
Set contentRoot, publicDir, and outDir in site.config.mjs, or overlay them from ../instance.config.mjs when the site is consumed as a git submodule.
The folder shape is opinionated (articles/, answers/, profile/, projects/, series/), but the location of that tree is yours.