Removed fortran cpp directory separation, just too many directories to go through

init, read, run, write

This is so we don't need a pointer to each array held within the actors.

Adjusted Command Line Parameters Use: Added more helpful output. Added ability to generate a config file.
Updated readme.

Merge branch 'summa_v4_changes' of https://git.cs.usask.ca/numerical_simulations_lab/actors/Summa-Actors into summa_v4_changes

Added command line arguments to output scripts.

Added instructions to resourceUsage script

Merge branch 'summa_v4_changes' of https://git.cs.usask.ca/numerical_simulations_lab/actors/Summa-Actors into summa_v4_changes

Merge branch 'summa_v4_changes' of https://git.cs.usask.ca/numerical_simulations_lab/actors/Summa-Actors into summa_v4_changes

Fixed issues with compiling with g++11.

Merge branch 'summa_v4_changes' of https://git.cs.usask.ca/numerical_simulations_lab/actors/Summa-Actors into summa_v4_changes

Also cleaned up the output strucutre and removed some of the calls to subroutines that are uneeded.

Can use json to pass state variable tolerances.
Can also just pass in atol and rtol to have all state variables set the same.

Moved the calls to fortran files to a singular file so we don't have to go
through C++ and Fortran for multiple functions.

This is now rectified

Moved read_attrb and read_icond to be called from job_init_fotran

 summa_SetTimesDirsAndFiles
 summa_defineGlobalData

The actors version now calls job_init_fortran as an interface which calls the SUMMA supplied subroutines.

Added the subroutines to the output_structure_routine for increased clarity.
Also removed the output structure specific file from the engine dir.

Replaced some messages with request statements.
This is to show the direct relationship the actors have in this request, instead
of relying on a send and send.

Used requests where it made sense in the actors. This is where the HRU
would send a message then wait for a response anyway. Instead of defining
messages for these cases we use request.