Document how to add CLI args for debugging

doc/help/projects/debugging.rst doesn't say how to configure the CLI arguments to pass to a program to debug. I found Issue 713, which says, "You can use x-run-opts inside flatpak manifest," but the example file it links to seems to use x-run-args, not x-run-opts.

This is only partially related, but when I tell Builder to open a project and select this folder: https://gitlab.gnome.org/GNOME/gtk/-/tree/master/examples/application3, for some reason, it highlights resources.c instead of main.c, and when I try to debug it, it somehow chooses to run demos/print-editor instead. Do I need to create a flatpak manifest for examples/application3 or is there an easier way to do this? Maybe this use case should also be documented?