Jonathan suggest here: Xcode Includes .xib files that have been deleted! that cleaning all targets and empty the caches will fix the problem with Xcode including deleted .xi
To delete all derived data and the module cache in /var/folders
use this little ruby script.
derivedDataFolder = Dir.glob(Dir.home + "/Library/Developer/Xcode/DerivedData/*")
moduleCache = Dir.glob("/var/folders/**/com.apple.DeveloperTools*")
FileUtils.rm_rf derivedDataFolder + moduleCache
This just solved a fatal error: malformed or corrupted AST file: 'Unable to load module "/var/folders/
error for me.