Simplify repository assembling and reference filtering #2849
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This PR contains the simplification parts of #2744.
These are code simplifications and a simplification in the logic of how to specify the filters.
Instead of providing inclusion and exclusion patterns, just use exclusions, but add a simple way to negate a pattern.
A negated exclusion is effectively an inclusion but it should be more clear how inclusion and exclusions work together, as the current definition can be potentially confusing: #2744 (comment)