Update output directory structure

[luisas]

Description of feature

Right now it is a bit overwhelming i find, there is many files and we could make it clearer to the use which are the important ones and not (and maybe merge some? we have for instance in seqinfo 3 files per sequence, maybe this could be one csv only about the information of the queries)

Also we output many files that are only meant to be intermediate (e.g. phylip format only used for fastme)