is whonix a free software system?
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https://www.whonix.org/wiki/Linux#Debian,_Fedora_and_Derivatives
If the gnu linux system you are running on a given computer is a free software system and you install whonix, then the system all together stays a free software system? Thank you.
As far as I can see Whonix seems to be a system distribution, in that case, I think it must first study and follow the GNU Free System Distribution Guidelines (GNU FSDG, https://www.gnu.org/distros/free-system-distribution-guidelines.html).
After that, they must send the project for review by following the steps described at "See something we missed?" (or something similar for your language) in https://www.gnu.org/distros/free-distros.html#NewDistro.
If there is a reviewer available and all goes well, then it should be listed as free distro.
Currently, the only free distros are listed in the following links:
For those which provide GNU packages: https://www.gnu.org/distros/free-distros.html
These don't provide GNU packages: https://www.gnu.org/distros/free-non-gnu-distros.html
Third-party repositories listing single-language packages, game addons, browser extension, virtual machine images/containers are all also subject to some part of the GNU FSDG in order to be included in any package management facility that might be in use by the distro. If the repositories that don't have written goals to follow the GNU FSDG exist in the package manager by default on a distro that follows the GNU FSDG, then it is probably a bug. In such cases, it can be worked around by disabling the default repository selection or any default recommendation and instead letting the user add any repository manually.