You have to right click + shift on the folder containing your project, then open the CLI and type "make". Then you'll get both .3dsx and .smdh files needed for the project to run on ninjhax.
I don't know for Linux though
I know next to nothing about programming but I assume you can change it in the main.c code, here:
u32 kDown = hidKeysDown();
if (kDown & KEY_START)
break; // break in order to return to hbmenu
Line 20 in the ctrulib template.
Anyway, it's a great tutorial...