its set to hide if no update, tho i got 2 updates that doesnt seem to happen anything when i try update and when i use the terminal with "sudo pacman -Syu " there is nothing to update.
Mod edit: removed screenshot showing 2 Flatpak updates in the Pamac GUI
Try running the following command in a terminal as a regular user (not with sudo):
flatpak upgrade
pacman does not handle Snaps, Flatpaks or AUR packages. It only accesses the official Manjaro repositories.
pamac on the other hand does handle the above ā in addition to the regular Manjaro repositories ā but after updating with pamac, it may be necessary to right-click the notification icon and refresh its database by forcing it to look for updates again.
i see, did not know. i did a search.
would this be a viable simple line to run in the future?
sudo pacman-mirrors --fasttrack && sudo pacman -Syyuu && flatpak upgrade
is there anything else i can add to make a all-in-one update command? and where in the .bashrc could i add the alias?
Hmm, no, one should never use a double uu with pacman unless explicitly advised by the Manjaro Team.
A double uu tells pacman to allow for package downgrades. This may be necessary under certain conditions, but if so, then only for isolated packages. You really wouldnāt want that to apply to the whole update process.
Likewise, one should also not gratuitously use a double yy, because this is unnecessarily hard on the servers, given that it forces a refresh of all package databases.
If you also have AUR packages, then I would suggest the followingā¦ 
sudo pacman-mirrors -f && sudo pacman -Syu && pamac update && flatpak upgrade
But even then still, be advised that the issue with the pamac notifier icon may persist until you right-click it and force a refresh. This is just due to how pamac works, and it is one of the recurring points of criticism against pamac.
You could indeed turn this into an alias, but whether you add it to ~/.bashrc or ~/.zshrc depends on what shell you use.
The default interactive shell for terminal sessions within the graphical environments of either of the three official Manjaro editions ā i.e. Plasma, GNOME and Xfce ā has for a couple of years already been zsh, but your installation may be older and/or you may have purposely selected bash as your interactive shell ā as have I myself as well, for that matter.
So perhaps it is best to add it to the bottom of both ~/.bashrc and ~/.zshrc, as followsā¦
alias fullupgrade="pacman-mirrors -f && sudo pacman -Syu && pamac update && flatpak upgrade"
And then, after reloading the configuration by sourceāing the file or by closing and reopening the terminal, the command fullupgrade will do exactly what it says on the tin. 
Now thereās a question.
You might take a look at Topgrade, as it isnāt a āproperā tool I generally run it after the main updateā¦
So for a system upgrade, āsudo pacman -Syuā gets it. To add AUR, then āpamac upgradeā followed by āflatpak updateā.
Using Fish make an abbreviation (otherwise an alias)
āÆ sudo pacman -Syu && pamac upgrade && flatpak upgrade && topgrade && exit
Topgrade is proper overkill though - I only run it after major updates.
If itās a fresh update and your mirrors arenāt great, or slow to sync, then I use continental flagā¦ it gets me best results and it doesnāt hammer servers so much eitherā¦
So abbreviation/alias for mirrors:
abbr mirrors 'sudo pacman-mirrors --continent && pacman-mirrors`
Remember also (with Fish at least) if you press Ctrl_R itāll put you in a fuzzy search, so just start typing ācontā will pull up the whole line from historyā¦ as will āupā bring up lots of upgrade/update lines to choose from.
@premier69 I use pamac gui for all my updates. I run refresh databases from hamburger menu after update completion, icon is updated after I close pamac gui
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