I’ve been banging my head against a brick wall for a few hours now on this, so I thought I’d post this for the benefit of anybody else searching:

If you are using the wonderful Cocoapods in an iOS project you’re developing, and you make one of your Pods load directly from a Git repository (perhaps GitHub) then there’s a little gotcha to be aware of: if the Podspec includes :submodules => true in the source section then it is necessary to manually add that to your Podfile too.

In my case, I’m hacking on my own version of the Bypass-ios Pod, so I had tried adding this line to my Podfile:
pod 'Bypass', :git => "git@github.com:andygeers/bypass-ios.git"

However, that was missing a few files from a submodule, causing compile errors like this:
'element.h' file not found

It feels a bit cumbersome, but instead it is necessary to write the Podfile like this:
pod 'Bypass', :git => "git@github.com:andygeers/bypass-ios.git", :submodules => true