file has been modified since the precompiled header was built

I faced this issue on OS10.10 with Xcode 6. I resolved issue by removing .pcm files.

To delete press ‘shift+command+g’ & delete all .pcm files or goto the folder ~/Library/Developer/Xcode/DerivedData/ModuleCache/ & delete all .pcm files.

Perform deep clean by pressing ‘shift+alt+command+k.

Hope it will work for you.