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Apologies for the lack of documentation. I need to work on that pretty soon to hand over the project to someone else, but I'm not sure if updated documentation will be sufficient for people outside our lab. I will update my answer when I've added this documentation.

1. It does not matter how the map was generated.
2. segbot_gui is not used in navigation. None of the launch files in segbot_navigation use it.
3. You've got the right command. You'll also need to supply a map file, as the default one won't work for you.

Good Luck!