fixed deserialization of phase diagrams

[jmmshn]

JSON reconstruction bug:
The problem is: Because MSONables from_dict was replaced, there is no recursive reconstruction of the objects when you hit el_ref . When you do as_dict -> from_dict in python everything looks fine.
but the object was never completely serialized.
If you completely serialized it like putting it into as json file or database then you cannot reconstruct the phase diagram.

[coveralls]

Coverage decreased (-0.7%) to 83.324% when pulling bb87db4 on jmmshn:pd_fix into 8a78794 on materialsproject:master.

[mkhorton]

Thanks @jmmshn!