Refactor internal data structure

[oschwengers]

Since its first draft, Bakta has come a very long way and has undergone many feature extensions, code additions and minor amendments. In order to keep the code base as lean & clean as possible, we restructured the internal main data structure and renamed and streamlined many variable names.

The main change (without breaking any external APIs) addresses the main data object which has been restructured and renamed from genome to data:

genome = {
        'genus': ...
        'species': ...,
        'strain': ...,
        'taxon': ...,
        'gram': ...,
        'translation_table': ...,
        'size': ...,
        'complete': ...,
        'features': {},
        'contigs': contigs
    }

Now:

data = {
        'genome': {
            'genus': ...,
            'species': ...,
            'strain': ...,
            'taxon': ...,
            'complete': ...,
            'gram': ...,
            'translation_table': ...
        },
        'stats': {
            'size': ...,
        },
        'features': [],
        'sequences': sequences
    }

This internal structure is now aligned with the document structure of the JSON result file. Also, former contigs are now denoted with the more general concept of sequences.