It would be useful if you explained how it is that you are using vim,
what you want to happen, and what terminal emulator you are using.
“command line copy and paste” is somewhat unclear.
The reason is that this likely depends on DE,TE, and vim version.
The vim version shipped with debian does not have clipboard support - check :echo has('clipboard')
But you can still have some copy/paste by using features in the terminal,
eg setting Xterm*selectToClipboard:true, then selection in xterm uses the
standard clipboard.
I never presume to speak for the Qubes team.
When I comment in the Forum I speak for myself.