What matrix client should i use and how?

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Is creating dedicated AppVM based on whonix-workstation with sys-whonix vm and installing Element there a good idea? Are there any potential security/anonymity flaws with it?

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I don’t see any security/privacy problems with that. However you should install Element in a (dedicated) template, not AppVM.

Alternatively, Element can be installed as a user, but I’m not sure how the updates will be handled.

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So i should create TemplateVM based on whonix-workstation with sys-whonxi as a net qube? Also, whats the reason to use TemplateVM and not AppVM?

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System files in AppVMs are not persistent. You can use something like flatpak or snap to install packages in the home directory. Some people don’t like them, and they utilize storage inefficiently (in QubesOS) because of how qubes work.

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Because for App qubes, the root filesystem is reset every reboot: Glossary | Qubes OS.

See also: How to install software | Qubes OS

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Thank you for your answer! I understand now

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