AlignTraj should have in_memory option

[wouterboomsma]

Expected behaviour

With the introduction of MemoryReader in 0.16, rms_fit_trj gained an in_memory option, which makes it possible to do in-place (in-memory) alignment. AlignTraj should have the same option.

Currently version of MDAnalysis:

0.16.0-dev0

[orbeckst]

This option should be added for 0.16.0 because rms_fit_trj() is being deprecated.