The MobileApp extension currently does very little: it contains some .less files from which the apps generate bundled stylesheets, and a JSON config file that the apps use to publish remote config settings. The .less files are likely soon to be consolidated with the rest of the mobile styles in MobileFrontend, and the JSON config file could easily be moved over as well.
Is it time to retire the MobileApp extension? Does it have any other consumers besides the WMF Wikipedia apps? What would it take to make this happen?