The inconvenient and somehow embarrassing truth for us – the malware experts – is that there does not exist any reliable method to determine if a given system is not compromised. True, there is a number of conditions that can warn us that the system is compromised, but there is no limit on the number of checks that a system must pass in order to be deemed “clean”.
Fortunately, you can always recover to a non-compromised state in the following way (and it’s not that complicated):
Indeed I am using Qubes without a command line (although I can use it when I want). However, certain things are not yet implemented in the GUI, e.g. volume revert. This is work in progress and, @sosqubesinstal, you can always help it.