The CDT parser is taking over 4 and a half minutes to parse the johntheripper code. This is a relatively small piece of code and should not take that long to parse.
This problem was found to be a bug in DOMFactory.java that was adding the same include paths multiple times. This was causing those include directories to be scanned multiple times thereby slowing the parsing. A new method was added to DOMFactory.java to check to make sure an include path has not already been added before adding it to the DOM.