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traj2box writes duplicated and wrong step indices when input files differ in length #194

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@galjos

The step offset is computed as len(traj) * (counter - 1), assuming every previously written file had the current file's frame count. With files of 3 and 2 frames:

steps written: 1 2 3 3 4     expected: 1 2 3 4 5

With a third file of 3 frames: 1 2 3 3 4 7 8 9 — step 3 duplicated with two different boxes, steps 5 and 6 missing.

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