The garuda-update (or update or upd is all the same) covers the following repositories by default: garuda, core, extra, multilib and chaotic-aur.
To update packages from the AUR repository at the same time with the system update, garuda-update -a is required.
This is also stated in the Garuda Linux Wiki:
Usage
Simply use
garuda-updateorupdatein your shell of choice. Both commands do the same >thing. Additionally, the following parameters are available:
Parameter Environment variable Description --aur/-aUPDATE_AUR=1Update AUR packages via paru/yay after system update.
and in the garuda-update help:
garuda-update -h
Garuda Update is Garuda Linux' preferred update solution.
The update script allows Garuda Linux to apply certain hotfixes and update automations for a smoother experience.
Usage:
garuda-update [options] -- [extra pacman parameters]
–aur/-a -> Update AUR packages via paru/yay after system update (UPDATE_AUR=1)
Or in short: always use garuda-update -a when AUR packages are installed.