Organize git repository

-gitignore a number of different files and directories
  -Ignore class files
-Add javadoc to the repository
-Add runnable jar file
output, help, documentation, maven package goal

-Output to csv file has been added
-A help/usage message is printed to indicate proper CLI usage
-Maven package goal has been updated to generate a runnable jar with a
short name
-Documentation/javadoc has been updated