ENH: Adds FileDictMixin

[VinzentRisch]

solves #346

• Adds FileDictMixin class that includes the function file_dict.

• For per sample directories it returns a mapping of sample id to another dictionary where keys represent the ID and values correspond to the filepath for each file.

• For files, it returns a mapping of ID to filepath for each file.

• To create the ID the specified suffix is removed from the filename. it is expected that the suffix is given with the used separator character like ".report"

• This mixin can only be added to classes with a pathspec attribute.

• For now it is added to Kraken2ReportDirectoryFormat and Kraken2OutputsDirectoryFormat.

• I also removed GenomeDataDirFmt and its genome_dict function and added FileDictMixin to GenesDirectoryFormat, ProteinsDirectoryFormat, LociDirectoryFormat and GenomeSequencesDirectoryFormat

This Mixin would also work with MAGSequencesDirFmt and MultiMAGSequencesDirFmt.

[VinzentRisch]

Hi @ebolyen @lizgehret
Could someone have a look at this?
The Idea is to have a mixin that can be added to any directory format that enables the format to use a file_dict function, similar to sample_dict function in MultiMAGSequencesDirFmt. So that the sample_dict function does not have to be added to any new formats.
This would be helpful for bokulich-lab/q2-annotate#212 and for my new plugin that I am working on right now.

Let me know if this makes sense to you or if you have any questions.