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You are in the middle of the bonus missions. But you can not do anything at this point except to continue with the main story. The bonus missions are ongoing releases of new content and the next one is currently worked on.

it IS in the main files of the mod the bonus missions do not require any cmd files in order to work and all you have to do to continue the main story is to return to the place where king and juni are waiting.

Tthe cmd file only will add reputation settings required to run random missions in the new systems and to make the new factions hostile to other already existing factions. (FL does not automatically update such information by default)