This fork of Theos is designed to work with apps on non-jailbroken iOS devices. You MUST have an Apple iOS Developer account in order to use this (for code-signing purposes).
You use it just as you would for a jailbroken device tweak (edit Tweak.xm then "make")
It integrates CydiaSubstrate
It integrates Cycript
It patches App Store apps (.ipa files) to load CydiaSubstrate, your tweak, Cycript, etc
It re-signs the patched app using your Apple iOS Developer certificate
You can then (re)install the patched app to your jailed device using XCode
You can remotely attach to Cycript using cycript -r hostname:31337
Requirements
iOS device
Apple Developer account
XCode with iPhone SDK
Patience and luck
Quick How-to
Extract and decrypt your target app. Save as a .ipa.
Check out this project
Change to the base directory for your new tweak
Run /path/to/theos-jailed/bin/nic.pl
Configure as you normally would for a regular Theos tweak
Once done, change into your new tweak directory
Edit Tweak.xm as necessary
Run make to build your tweak
Run ./patchapp.sh info /path/to/your/file.ipa
Take the information from that and use the Apple Member Center to create a matching Provisionin Profile.
Save the Provisioning Profile somewhere on your computer.
Run .patchapp.sh patch /path/to/your/file.ipa /path/to/your/file.mobileprovision to inject the tweak into your .ipa
Install the patched .ipa back onto your device using XCode.