We agree that CDT’s Problems View default behaviour is far from being really ergonomic and intuitive.
Please be sure we are aware of that and we will try to tune this behaviour (or make it more easier to tune) in a future release.
Meanwhile, you can tune it by yourself in some clicks:
In the View Menu of the Problems View, go to Configure Content.
In the Configurations list, select the Errors/Warning on selection one, and click OK.
–> from now, the problems view content is related to the currently selected item in the Prject Explorer. You can select a project to get all its errors, or select a given file to focus on its specific errors.
From now, you just need to order the problems by Location, to get something similar to the true compiler output.