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Per this discussion, https://forums.whonix.org/t/fixing-whonix-boot-issue-after-securing-qubes-root-auth/3155/8 Whonix executes sudo commands in non-root startup scripts which causes pop-up auth prompts to appear while Whonix VMs are starting. The problem is partly due to sudo parsing sudoers.d entries in alphabetical order, and some later configs cause earlier ones to get overridden. Adding the right permissions to a lexically 'last' filename resolves the issue.
Qubes OS Documentation
Canonical URL: https://www.qubes-os.org/doc/
All Qubes OS Project documentation pages are stored as plain text files in this dedicated repository. By cloning and regularly pulling from this repo, users can maintain their own up-to-date offline copy of all Qubes documentation rather than relying solely on the Web.
For more information about the documentation, including how to contribute, please see the Documentation Guidelines.