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CLI and GUI still produce different results in beta8 #1049

@pjreiniger

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@pjreiniger

Same idea as #1006.

It appears in beta8 that the the GUI is writing out .traj files with "version": 1, while the cli writes out "version": 0. There is also a problem with one writing out 0 and the other writing out -0 in certain situations.

Attached diff from generating with the gui as the base, then running the cli on top
beta8_example.patch

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