So how do I to install flatpaks? (Install flatpak CLI in the template and use it on the qube?)
~~Dunno what is the proper way to install flatpaks, those few times when I actually need to use a flatpak, I just download it to an app qube and then launch it from terminal (I guess that's what you're doing as well?). I use Arch [btw] for some of my qubes, and installing mullvad browser is easy thanks to AUR :)~~
Ah sorry, I actually confused flatpaks with AppImages. I don't use flatpaks at all :(
When I'm doing a Kali template it doesn't give me all the apps that are present in Kali.
Have you installed them in the template?
And if I want to use Parrot?
If there are no templates available, you will have to either create one or use HVM. Can't help you with either though
Maybe those apps are not installed by default in the template? Launch a terminal in the template and try to install ettercap and wireshark from there.
Never tried that, and I couldn't find anything about installing templates from local files on qubes wiki :(
Try
qvm-template
command in dom0 terminal and see if there are options to install template from local files there.