NetRadiant level editor and q3map2 map compiler now supports them. This was one of the things preventing to edit map against released Xonotic assets. The other missing thing required to ditch the Xonotic mapping package is the support of the dds/ prefix, that will be addressed later.
The support is minimal but good enough for the need: it only supports symbolic links within the same package and simple relative paths (for example: ../../textures/castle/brick.png).