Do not apply overrides to a root application.

[ferd]

Overrides should apply to a layer below where they are declared. This
patch makes it so if the project root is an application (i.e. it isn't
'root' and therefore not an umbrella project), we omit applying
overrides in rebar_app_discover.

This in turn required changing a bunch of tests, because all the tests
worked with the idea that all overrides applied to all apps to validate
that they get inherited properly. The changes re-structure the cases so
they are written with an umbrella app, demonstrating that the changes
stick.

This addresses #2082 partially (still need to add docs)

The big risk here is whether any important project in the wild
relied on the bad application of at-large overrides to make their main
app in a non-umbrella work. I'm thinking the chance is low enough (it
would have been accidental and not "ah yes this is how the feature ought
to work", IMO) that this PR might be worth it.

[tsloughter]

I'm a little worried about it but it makes sense to do.

[ferd]

At the very least it should have no effect on any dep I think, since those overrides would never have been applied to themselves in the first place (they don't go through app discovery on the first build if they haven't been fetched?).

At worst, we'll break the top-level project build only, but the deps would already have been broken. @tsloughter I think this de-risks it a lot since at least we don't risk breaking deps of existing projects, just the roots. That significantly reduces the network effect.