Applied @greg2001 changes as made the program friendlier for an automated build environment

[briandilley]

• Applied pull request #2 from @greg2001
• Added support for passing class files in to have headers generated (this made it easier to integrate with a gradle build process)
• Made a few more modifications to make the header generate identical to the javac -h ... command
• Added caching for ClassReader
• Made it possible to send classes in that don't have native methods, these are just ignored (this made it easier to integrate with a gradle build process)