It would be beneficial to allow the machine and user cert stores to be read/written from/to arbitrary locations, rather than the currently hardcoded locations in mcs/class/Mono.Security/Mono.Security.X509/X509StoreManager.cs - e.g. this is needed to allow Flatpak MonoDevelop to read/write Mono certs from the standard location, whilst still storing the MonoDevelop config in a special sandbox per-app location. As-is, Flatpak overrides XDG_CONFIG_HOME, which causes Mono to use a special per-app config directory of ~/.var/app/com.xamarin.MonoDevelop/config/.mono/