Remove all magic initializations of config

[percyfal]

Currently we're setting references, indices etc via functions in a manner that is hidden from the user. All these functions (annotation, index, ref, etc) should be placed in metadata-specific modules (e.g. cloudbiolinux) and explicitly called by the user if so desired. This enforces the user to explicitly list all indices, refs etc or to knowingly import a function from a module. Moreover, this would ensure that all the rules in fact could be used without invoking snakemakelib.