1098891: Update repos, persisting local settings when possible

remove tests that are no longer valid
1098891: Apply overrides to mutable properties
Cache overrides when RepoFile is written

This way we can verify whether or not the source of a repo value
was an override that has been removed, vs a manual edit
correct repos --list behavior
update existing repos with non-default overrides
Some minor comment updates.
Merge pull request #947 from candlepin/ckozak/repos_update

1098891: Update repos, persisting local settings when possible