I haven't used AppGameKit v2 on Linux (so the following could be wrong) but the typical way that Tier 2 projects work is that there's a source file (maybe interpreter.cpp idk what it is called anymore).
Inside this source file you should see 3 functions:
void app::Begin() - called on app start up
void app::Loop() - continuously called
void app::End() - called on app exit
You'll have to design your app around these functions e.g