Merge Run and Standard Run base classes to a single base class

[aanil]

We have 2 base classes for Illumina runs, Run and Standard_Run. This is an artefact from when we only had MiSeq and Run dealt with only MiSeq runs. Standard_Run used to be HiSeq_Run which then inherited from the base MiSeq run class.

When there was a partial code cleanup and renaming of classes, the MiSeq specific methods were not moved to the new MiSeq_Run class.

We should move these methods to the MiSeq_Run class and merge the current Run and Standard_Run to create a generic base class.