[layers v2] Make CLI commands layer-aware

Part of #9765.

Quite a few azd commands already accept a layer parameter. For commands where it would be unambiguous, making the first named argument a layer is an easy choice.

For commands where it would be ambiguous (for instance, `azd deploy `) we need to consider if it'd be sufficient to just add a `--layer` switch.

Another consideration — if the user does NOT specify a layer, what is the right behavior?
- Use a "default" layer? Assume a flat layout? (flat being the existing pre-layer format)
- Does the result matter if they're using the old 'flat' infra/services layout?
- (probably more)