Some basic USE flags would be nice, even if it's just used for documenting which configure-flags and inputs are needed for which feature. I think this would also resolve the sorting inputs alphabetically issue, since there would be real metadata there instead of just a source comment.
> I think that's a case where the knowledge embodied by the comments and > ordering is worth more than sorting alphabetically. This requires python2-sphinx to be installed when building even if you are not interested in the doc output.