I've tried to add this repo and get the message that the hostname cannot be found. Is this repo still active? If not has the XCon beta been made available elsewhere?
I will certainly take a look at Flex as I really do not want to have to restore and re-jailbreak this iPhone again.
I did find the proper repo link for XCon and was able to get one of the older beta versions installed however the beta versions are causing the same issue the current versions are which is after installing the App Store will not load at all, it completely borks the native email app, and is probably causing other problems I haven't yet located.
Uninstalling XCon puts everything back at square one with the apps loading however the app store update all link is dead and hitting the update button next to an app just launches the app without updating it.
Also, just for due diligence I'm on an iPhone 4 with iOS 7.0.6, jailbroken obviously. The app that brought this issue to my attention was the Mimecast mobile app, which is a service we use for our email filtering at work if no one's heard of it. I've not found any other apps displaying the "unable to run on jailbroken device" message, yet, so wondering if the Mimecast app left something behind in the system still identifying my phone as jailbroken.