development dependencies that should be regular dependencies marked as transitive dependencies

[fpgmaas]

Describe the bug

Transitive dependencies now catch multiple issues:

• Transitive dependencies, as it should. Package A depends on B, B is imported, but A is added as dependency.
• Simple user misconfiguration; files that should be run with dev dependencies are scanned. Can happen e.g. when user overrrides the ignore_directories configuration, but does not add tests in the list.
• A dependency that is wrongly marked as a development dependency (i.e. it is imported within the codebase).

Expected behavior

We need to either catch these separate issues, or improve logging to reflect the above, so the user knows what to do. It would be relatively simple to also read the dev requirements and warn the user if the above happens.