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System messages differ from e.g. validation messages in a number of ways. First, they report important system status changes. As such, they have to be displayed more prominently, but should also be used scarcely. Second, the context of a system message is usually gone once it's being shown. As an example, a process running a longer time might fail eventually, or a regular background cleanup job has discovered an oddity, which requires a warning to be displayed to the user. The message thus shows up in any context. By contrast, a validation message can still be visually related to the field, which caused the problem, when it is displayed.
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