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Separate Pacman upgrade and AUR Upgrade by default
Currently When performing a system upgrade, Yay will first refresh the database then perform the repo and AUR upgrade. This allows Yay to add some features such as better batch interaction, showing potential dependency problems before the upgrade starts and combined menus showing AUR and repo upgrades together. There has been discussion that this approach is a bad idea. The main issue people have is that the separation of the database refresh and the upgrade could lead to a partial upgrade if Yay fails between the two stages. Personally I do not like this argument, there are valid reasons to Yay to fail between these points. For example there may be dependency or conflict issues during the AUR upgrade. Yay can detect these before any installing actually starts and exit, just like how pacman will when there are dependency problems. If Yay does fail between these points, for the previously mentioned reasons or even a crash then a simple refresh will not cause a partial upgrade by itself. It is then the user's responsibility to either resolve these issues or instead perform an upgrade using pacman directly. My opinions aside, The discussions on the Arch wiki has reached a decision, this method is not recommended. So to follow the decided best practises this behaviour has been disabled by default. This behaviour can be toggled using the --[no]combinedupgrade flag It should be noted that Yay's upgrade menu will not show repo packages unless --combinedupgrade is used.
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