Only use JSON output of compareMS command line #64
Description
The current version of the compareMS2 command line can produce output in both JSON format and in the original text based format. Both output formats are used in the compareMS2 GUI and compareMS2_to_distance_matrices software.
This is undesirable, because now output in both formats must be stored for caching, and both output formats must be maintained.
To solve this, the compareMS2 GUI and compareMS2_to_distance_matrices should only use the output in JSON format.