[docs] clarify when to use message and when to use progress(..., permanent=True)

[lengau]

What needs to get done

Clarify when a developer should use message or when they should use progress.

Example: Which is the correct way to show a warning?

Why it needs to get done

User confusion: canonical/craft-application#302 (comment)

[mr-cal]

As discussed as a team, emit.message() should only be used for the real output of a command.

For example, snapcraft plugins should use emit.progress(permanent=True) for the deprecation notice to use snapcraft list-plugins and emit.message() to print the list of plugins.

Assigning this to @tigarmo, who is going to clarify this in the docs.

Long-term, the correct path forward will be #256