Refactor config-building in lib.rs's run_with_repo

[blairconrad]

From #143 (comment):

I have a weak dislike for [the recent config refactoring in #143 …] refactors are a matter of taste after all. if i was going to spend time cleaning it up, i would probably make a function in config.rs that takes a Config and returns a new Config with flags unified and repo defaults applied (then run_with_repo can go back to taking an immutable Config). maybe dedup the config fetching code too, but that might require a macro.

[blairconrad]

@tummychow, so far I have only read the word "macro" as pertains to rust, but if you're not in a huge rush, I'd like to try to fix this. I caused (or at least contributed to) the problem after all.

[tummychow]

i'm not too committed to the idea of using a macro for this, only if it leads to fewer loc. it's annoying to have like 50loc of "get this config option! it's this type! default it to this value!" but it would be worse to have a 200loc one off macro just for this