[akutuva21]

This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.

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PR created automatically by Jules for task 4118980527979395642 started by @akutuva21

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