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My point is that I work like that with current IDE's when using Qubes OS.

What I suggest is that Flatpak could provide something similar, by having a completely separate filesystem used by the tool.

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That would need UI similar to Qubes that would have to be built and integrated probably on the IDE side. Purposefully, flatpaks don't typically ship a whole OS like Qubes VMs do, so the gap has to be filled somewhere.

Most VMs in Qubes does not come with a full OS. They're based on templates, which isn't too different from the system packages of Flatpak.

Also, Python developers seems to be dealing with this stuff on a daily basis with virtualenv, so this isn't something new.

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