Added ph.x functionality.

Now can run dfpt jobs. Uses a new list phxlist.py. Also run parameters were factored out to runlist.py.
Can use dependent pwx job by passing a pwx object with phx(..., PWX=pwxObject). A example file si_ph.py
showing this dependency was created.
Added q2r funcitonality. Added run params to object initialization.

Now execute the q2r (phonon qpoint to real space) transformation of the dynamical matrix. Can
take a phx object as a dependent. Also all classes (pwx, phx, q2r) can take run parameters in
their object initialization. This helps with dependencies so the dependent jobs do not resort
to the defaults set in qepyrc.