Add position_in_additional_file_patterns to options and parser #977
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When running annotations on files that match additional file paths the default position is not observed and it will always default to before. Essentially this line resolves to
position_in_additional_file_patterns
in this case but the option parser does not account for this case.This PR allows that option to be parsed, set and defaulted so that that files that match additional patterns can have annotations set at the bottom of the file.