Pass params by file, manually set param values.

Add the ability to pass parameter values by file rather than all on the command line
    - The file name is passed on the command line instead. See the Reference docs
      on TestProgram  for usage (example 3).
      
Add the ability to manually specify the parameter values
    - These values are used directly to evaluate the test program. This functionality
      is useful when the paramter samples are generated by an external program and
      it is necessary to use those exact samples. This contrasts with the current 
      implementation which fits a pdf to the samples provided and samples from the
      fitted pdf. This new functionality has some caveats. See the use_samples_val
      of the CustomParameter docs.
      
Clean up some code for the Morris method.      
      
Improve echoing of commands to the output hdf file.

Add some exception handling in util.py 

Update some doc strings and internal comments

Update readme