[WIP] Doing the right thing with box information

Currently we're reading the box information from all of the trajectory formats, but just ignoring it mostly. Some of the formats (XTC and the setters for OpenMM) use the box vectors but others (DCD, AMBER NetCDF) use the lengths and angles.

We need to do the right thing to represent the information inside of the trajectory object and support both formats. So far I've just added the code to convert between the two.