[docs] clarify when to use `message` and when to use `progress(..., permanent=True)`
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Issue body
### 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: https://github.com/canonical/craft-application/pull/302#discussion_r1562935131
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