Clean up temporary files

[iimog]

ChloroExtractor creates multiple large temporary files (especially the jellyfish files can be multiple GB in size). An option like --clean to remove those temporary files and only keep the final output would be convenient. Alternatively the cleaning could be the default and an option like --keep-intermediates could be introduced.

[greatfireball]

I would suggest the following behaviour:

1. default procedure should be cleaning of all intermediate files incl. assembly folder etc. (default or triggered by --no-keep
2. single --keep will keep the assembly folder, but will remove other intermediate files
3. at least two --keep (similar to an enhanced verbosity mode by multiple --verbose) will keep all intermediate output files

opinions?

[iimog]

In my opinion this is a good solution.

[greatfireball]

It is filed for version 2.0.0