Trajectory continuations need testing

[eirrgang]

We need to make sure that we keep a good handle on the file management for restarted simulations and for simulation input that has been repurposed from simulation output.

• Test appended and non-appended continuations that the time frame recorded in the output files is as expected.
• Test that atom positions in the restarted simulations are closer to the atom positions at the end of the previous segment than to those of the TPR file.

Relates to issue #40, #79, and PR #126