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I am a beginner, running my first Flask app through pythonanywhere. Is there anything I need to concern myself with about whether folders can be publicly accessed. Is basically only the folder listed as static accessible externally? Are my /templates folder my app code and any associated scripts generally safe from prying eyes if not in static folder?

Any files not in a static directory cannot be accessed through your site

Yes, exactly. We also have some further hints and tips about security on this help page.