I'm having issues with an iPhone 5 on iOS 8.0 JB'd. (I want to remind this is a untethered JB.)

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Last afternoon I was organizing through some apps and tweaks to optimize this phone. Nothing too crazy as I was just uninstalling. I got to a part where I wanted to manually install the .deb of YT . (I archive .debs.) I accessed the Cydia Auto-Install directory on this phone, placed the .deb in that location, rebooted phone, and upon reboot I noticed some system apps went missing from the Home Menu (and from the Settings line-up). Researching showed that I'm missing apps such as Mail, Calculator and some others... This is iOS 8, I cannot redownload Apple apps like newer iOSs can. And this .deb of YT has never cause such an issue like this. So I can't suspect it. Now what's interesting is that the apps are still located in their /Applications directory... I just need a way to make them recognizable again.

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I'm open to suggestions that may help. I'd REALLY like to refrain from updating iOS since this is an iPhone 5 and iOS10 would just kill it. I thought of Semi-Restore but I'd like to get some opinions before trying anything.

EDIT: These are the missing Apple apps: Calculator, iBooks, Health, Mail, Maps, Podcasts, Safari, and Weather.