I forgot which app it was (think it might've been custom theme installer), but I had one app that wouldn't install no matter what, so I had to use qcma to get it on to the system. it worked.
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btw, make a backup of ur0/shell/db/app.db so you never have to go through this shit again.
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you might also want the appmeta on ur0's root. that contains icons, backgrounds, etc for the installed titles. default app stuff is located in vs0 iirc.
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another btw, the app.db is what makes the apps show up on the livearea, so it's good to have. they use page/position. the page is kinda obvious and position goes from 0-9. it's kinda hard to determine page with folders, since they're like 20+, but the first page is either 3 or 4, I forgot. that's how you can see if something is installed. if two things are installed to the same page/position, one or both won't appear, forgot that too, but it won't harm the system. that's in the appicon table with the name and location of the icon. the appinfo table is mostly stuff from the param.sfo, so it's very important. you don't need to know all that, I just find it interesting. it contains your configuration (where things are located, folders, folder names, etc.). that's why you should back that up.