Conversion utils XYZ<=>netCDF

(Apparently merging all my recent stuff on XYZ file to my master *changes* my previous pull request, instead of letting me generate a new one. But this is basically a new issue from what we had before.)

Includes nose tests, a real test file (accounting for about 3/4 of the lines added), and several fixes to small bugs in choderalab/master branch.

Round trip (through two calls of the conversion script) isn't bitwise identical on the files, but inspection shows that it is working well enough.

Left to do: 
* ~~support translating multiple trajectories~~
* support topology directly in netCDF file we save (Am I correct that topology doesn't currently go to storage, @jhprinz ?)
* ~~better docs/tests.~~ (Always need better docs/tests, but I'm happy with what I've got)