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If the app is explictitly given access to a subdirectory of one of the xdg config/cache/data directories, with read-write (or create) access, then also bind-mount that directory into the corresponding .var/app/$APPID directory. This allows apps that want it to keep re-using global directories for storing per-app information. For instance, if your app uses "~/.config/foo" to store configuration data, then you can use --filesystem=xdg-config/foo, which will look for the directory, and if it exist, let the app access it, as well as mirror the content in ~/.var/app/$appid/config/foo. You can also use a ":create" to enforce the directory to be created and thus always do the mapping.
Flatpak is a system for building, distributing and running sandboxed desktop applications on Linux.
See http://flatpak.org/ for more information.
Read documentation for the flatpak commandline tools and for the libflatpak library API.