Add index and minify command line arguments

[mshadbolt]

• added a command line argument --index to enable the 'indexed' output json

  • For large datasets, the index file can get quite large and in a lot of contexts, is never looked at or used by a user.
  • default behaviour is to no longer output this file

• added a command line argument --minify to enable 'minification' of jsons,

  • Removes white space and new lines to reduce the file size of the output
  • impacts human readability of the file so default behaviour is still to output, indented 'pretty' json

[daisieh]

Looks good! I removed one space from a doc string.