Solution 1:

Finally got this working!

Tested with a IPA signed with cert1 for app store submission with no devices added in the provisioning profile. Results in a new IPA signed with a enterprise account and a mobile provisioning profile for in house deployment (the mobile provisioning profile gets embedded to the IPA).

Solution:

Unzip the IPA

unzip Application.ipa

Remove old CodeSignature

rm -r "Payload/Application.app/_CodeSignature" "Payload/Application.app/CodeResources" 2> /dev/null | true

Replace embedded mobile provisioning profile

cp "MyEnterprise.mobileprovision" "Payload/Application.app/embedded.mobileprovision"

Re-sign

/usr/bin/codesign -f -s "iPhone Distribution: Certificate Name" --resource-rules "Payload/Application.app/ResourceRules.plist" "Payload/Application.app"

Re-package

zip -qr "Application.resigned.ipa" Payload

Edit: Removed the Entitlement part (see alleys comment, thanks)

Solution 2:

The answers to this question are a little out of date and missing potentially key steps, so this is an updated guide for installing an app from an external developer.

----- How to Resign an iOS App -----

Let's say you receive an app (e.g. MyApp.ipa) from another developer, and you want to be able to install and run it on your devices (by using ideviceinstaller, for example).

Prepare New Signing Assets

The first step is to attain a Provisioning Profile which includes all of the devices you wish to install and run on. Ensure that the profile contains a certificate that you have installed in your Keychain Access (e.g. iPhone Developer: Some Body (XXXXXXXXXX) ). Download the profile (MyProfile.mobileprovision) so you can replace the profile embedded in the app.

Next, we are going to prepare an entitlements file to include in the signing. Open up your terminal and run the following.

$ security cms -D -i path/to/MyProfile.mobileprovision > provision.plist

This will create an xml file describing your Provisioning Profile. Next, we want to extract the entitlements into a file.

$ /usr/libexec/PlistBuddy -x -c 'Print :Entitlements' provision.plist > entitlements.plist

Replace The Provisioning Profile and Resign App

If you are working with a .ipa file, first, unzip the app (if you have a .app instead, you can skip this step).

$ unzip MyApp.ipa

Your working directory will now contain Payload/ and Payload/MyApp.app/. Next, remove the old code signature files.

$ rm -rf Payload/MyApp.app/_CodeSignature

Replace the existing provisioning profile (i.e. embedded.mobileprovision) with your own.

$ cp path/to/MyProfile.mobileprovision Payload/MyApp.app/embedded.mobileprovision

IMPORTANT: You must also resign all frameworks included in the app. You will find these in Payload/MyApp.app/Frameworks. If the app is written in Swift or if it includes any additional frameworks these must be resigned or the app will install but not run.

$ /usr/bin/codesign -f -s "iPhone Developer: Some Body (XXXXXXXXXX)" --entitlements entitlements.plist Payload/MyApp.app/Frameworks/*

Now sign the app with the certificate included in your provisioning profile and the entitlements.plist that you created earlier.

$ /usr/bin/codesign -f -s "iPhone Developer: Some Body (XXXXXXXXXX)" --entitlements entitlements.plist Payload/MyApp.app

You can now rezip the app.

$ zip -qr MyApp-resigned.ipa Payload

Done

You may now remove the Payload directory since you have your original app (MyApp.ipa) and your resigned version (MyApp-resigned.ipa). You can now install MyApp-resigned.ipa on any device included in your provisioning profile.