In my project, I\'ve include a full \"shared\" folder by link (not copy) that is outside my project folder.
In the .pch file, I have #import \"MyStandardHeader.h
I've seen this too: files that clearly exist get wonky. Oddly, sometimes it fixes itself. It may be an Xcode bug, since the build always succeeds. I've had success with touching the file. sometimes a clean helps. and sometimes quitting xcode helps.... Voodoo really.
You could try to remove the index by deleting everything in ~/Library/Developer/Xcode/DerivedData
That directory is a combined version of the old Build and Intermediates directories from Xcode 1,2 and 3. Basically it's all the temporary and generated files from your project: object files, indexes, etc.
Merely closing XCode (6.4) fixed my particular case of this issue. I opened it back up, cleaned the project, and built. Warnings were gone! Before I closed XCode, I cleaned and built and the warnings would not leave. So something about closing XCode did it. Hope this helps others!
If deleting data and Prefix Header path doesn't work then, try to click on the File (that is not found) in the Project Navigator and uncheck the target under Target Membership in File Inspector. Then deleted the files from Project Project Navigator and add again. This is the only thing that worked for me.
I tried the steps mentioned above, but to fix the error I had to remove the file from "Copy Bundle Resources" in the project "Build Phases".
I deleted the #import, then moved to a different line and used autocomplete to reenter the import. That error and all others like it disappeared. Strange bug.
Another thing to try -- just deleting Derived Data wasn't working for me, but this did:
Delete Derived Data using the Organizer window, Projects tab.
In your target settings delete the value (path) set for "Prefix Header"
Close XCode and restart. Reload your project. Let it re-index.
Restore the "Prefix Header" setting.
What a major PITA.