Just follow the same problem and find a solution for yourself. Sorry for such a late reply, but hope this can help someone else.
There is an implemented Ruby game from a guy from the Cocoapods team to disintegrate Cocoapods from the project. You can find it here. If you de-integrate Cocoapods from your project using this gem and then run pod install , you will see that all phases of Cocoapods build are added to your project.
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