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Fix Updater only restarting sys-* qubes
After an update to qubes-vm-update [1] (which the SDW updater uses under the hood) `--restart` was changed to only restart `sys-*` qubes. The new qubes-vm-update flag --apply-to-all has the behavior we intend. Fixes #1127 [1]: QubesOS/qubes-core-admin-linux@93078d0b
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