I guess i shouldn't install packages this way

I was having a lot of problems with my menu and applications until i removed all of my packages that were put in /boot/home/config/packages then everything started to work fine after that, except for the occasional freezes, but I think that might be a hardware issue that i’m having i mean, it’s a gaming pc, but it’s starting to approach the age of ten years and I think it could also be my OS install
Considering that I am using the development build of haiku

If a package is existing in /system and in /home trees then, the one in /home tree is used.
HaikuDepot, SoftwareUpdater or pkgman are aware of packages in /home tree but are not managing them. Therefore an “old” package in your /home tree can block the update of a lib in /system tree that it is depending on to not be broken. So, you must clean up things there from time to time. And among things to check are the dependencies of packages that you’re putting there.

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ah i see that is the real reason why