Changes

Pushing k loop down through clip_variance_level.
This change is for the files advance_wp2_wp3_module and advance_xp2_xpyp_module.
In order to make this change, I added a new variable in the upper-level subroutine
that is an array version of the variable 'threshold' and passed it along to the lower subroutine.
The loop is still present in order to calculate the values of threshold, however, the calls
to the subroutine is outside of the loop. The only calculations inside the loop is for
and intrensic function, max.
All results are BFB identical for default case along with l_stats_samp being set to true.
For ticket #951.

Udpates to make it possible for us to keep certain parameters equal to each other during tuning.

Includes:

* a new subroutine in parameters_tunable.F90 that will read a new namelist in the error_*.in files
* updates to src/error.F90 to make sure the intended parameters are held equal throughout the tuning run
* updates to src.error.F90 to print the variables that were held equal at the end of the tuning run, together with their beginning and ending values, and updates to ensure that the new tuned values are copied into the new paramters_tunable_*.in file so they can be used for plotting or restarting the tuner.
* includes several simple error checks

See #939.

Updates to improve error checking for the tuner, updates to comments.

See #939.

Getting rid of a duplication of code.

Updating name of l_vary_params_together flag to l_keep_params_equal, since this is probably more clear and also is more consistent with my comments in the code.

Further tuner updates.  These updates introduce the option to give a minimum value for tuned parameters.  Error checks are included.

See #939.

Removing an old comment

Updating some comments related to the tuner updates.

See #939.

Update README

Minor updates requested in pull request: renaming a variable and adding some comments.

See #939.