Lots of minor cleanup. Replaced typedef with using throughout.
Created read and write methods for Sweeps class.
Modified Permutation class to allow arbitrary number of entries.
Added a new version (needs testing) of fitApplyMPO which takes a Sweeps parameter for more fine-grained control and noise feature.
Added new version of readFromFile which optionally takes constructor args for newly created T object and returns the object read from disk.
Merge remote-tracking branch 'upstream/develop' into develop