I have written minimal networking qubes sys-net-{eth,wifi} (salt states here), but I just realized that R4.2 doesn’t have the custom-persist feature I was trying to use. So in trying to understand why my sys-net-wifi preserves network manager connections, I discovered both my networking qubes have /rw/config/NM-system-connections for persisting these connection files. I can’t find any documentation describing what feature or service configures this persistence. Does anyone know?
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Answer: qubes-core-agent-network-manager (source).
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