Robert Langdon: [reluctantly] Surely such a travesty has never occurred.
Why would one even want to do this? Let's say, you're doing some sort of zomg malware research and you want to verify something. You can either use a jailbroken phone, code signing is kinda moot there, or a real phone :)
VT samples of iPhone apps are sometimes encrypted, tough luck then. Most of the time they are already stripped of DRM. So you can download one and rename it to *.ipa. Then the fun begins.
I'll assume you already have a working Xcode setup and can sign and run a test app on your device. If not, Google it, there are bazillions of how-tos on that topic.
The best and most fool-proof application for re-signig is iReSign, or you can do the signing manually, using commands similar to ones here (codesign is the main one, duh) or here. IReSign requires you to chose the application to resign, the certificate and the profile. Entitlements can be usually omitted, the app will attempt it best at recovering the ones required. The ID field can be left unchanged if your certificate allows for * to be signed, otherwise change it to something that you can actually sign for.
- If in the process of re-signing VT ipas you get "Getting certificate ID's failed" from iReSign and the cert list is empty, don't worry, this is temporary after 16 Feb 2016 because Apple's root cert has expired. To save you some googling - http://stackoverflow.com/a/35399656 ("Show expired certificates" in keychain, then delete the old ones, install the new one).
- iReSign needs the correct provisioning profile that applies both to the ipa file being re-signed and your iPhone. It looks like setting them is a little contrived, what finally worked for me was using “iOS Team Provisioning Profile: *” from Xcode. Download it, or a similar one from developer centre. It massively depends on your particular setup, though. The simplest way to test yours is to create a base iOS project with Xcode, fiddle with settings (do not leave them on "Automatic") in "Build Settings"->"Code Signing" and try "Project"->"Run" for your dummy project. If it does install and run, use the same identity and provisioning profile for iReSign.
- You are likely to get (if you install via Xcode, iTunes install will silently fail) "Can't install application. The Info.plist for application at... specifies a CFBundleExecutable of ..., which is not executable" at some stage. This is because VirusTotal samples do not maintain Unix file permissions and the main executable needs to be, well, executable. Unpack and "chmod +x" then repack the ipa, either before or after re-signing: https://github.com/maciekish/iReSign/issues/45.
- Sometimes troubles with signing are due to a mismatch of the certificate in the provisioning profile and the keys you have. See here for how to check the DeveloperCertificates in the provisioning profile (and don't forget to split lines in your .pem to 63 char lengths). Then again, overall signing is described in a million places on the Internet :)