and in what place should this be done?

Currently you pass a function to the Database initialization (db.load(), the filefetcher_t), which is passed to read files. When this is implemented, nyan would get passed an object of abstract type that provides file opening/reading features. This abstract type is then made concrete in openage by implementing it (i.e. a subclass) that calls to openage's filesystem abstraction features (but that doesn't concern this issue directly of course, since we only need to provide an api class).
If we just want to replace the filefetcher_t for now, the simplest variant is:

class nyan::Filesystem {
public:
    virtual nyan::File open_file(const std::string &filename) = 0;
}