Greatly improved resource handling
- Improvement:  Completed all TODOs in ResourceHandler
- Improvement:  App now only removes files from the temporary directory that aren't resources files (ie the files generated during compiling)
- Improvement:  Improved the readability of ResourceHandler, CommandLineInputProcessor and GroovyToExeConverterRunner
- New feature:  App now writes its gradle.properties file to the temp directory and checks it when running and if there's a version mismatch the app will extract/overwrite all necessary files
- New feature:  App now ensures all necessary files exist before permitting execution