How to remove one of the cocoa pods plugin from Xcode project

Remove the pod from your podfile, then run pod install again.

You have to edit the Podfile ($ emacs Podfile in terminal.app) and remove the line pod 'nyximagekit' from it. (ctrl+x, ctrl+s to save, then ctrl-x, ctrl+c to quit emacs)

Once you did that, run pod update and it will remove nyximagekit from your project.