Gaussian-step

* Added ability to calculate the Wiberg bond order matrix and optionally use to set
the bond orders of the structure.
* Enhanced the optimization for transitions states to capture the vibrational
analysis if the second derivatives are calculated, and report on the stability of
the structure.

* Fixed a bug that caused the plug-in to fail when used in a loop.
* Improved the creation of the gaussian.ini file to both work better and keep the
comments in the file.

2024.6.5: Cleaned up logging from code.
* The logging was a bit aggressive, so moved most logging down to the debug
level. This will make the output of e.g. geomeTRIC more readable.

2024.5.31: Added optimization of transition states, and...
* Corrected implementation of composite methods (Gn, CBS-x) to handle optimization.
* Added target of the optimization to allow transition states and saddle points.
* Corrected a bug in handling the maximum number of optimization steps.
* Corrected bug determining if optimization completed properly.
* Corrected bug handling the composite method results.

* Added the number of steps for the optimizations to the results that can be output
to tables, variables, etc.

* Updated to new calculation handling, with ~/SEAMM/gaussian.ini controlling access
to the installed version of Gaussian on the machine.
* Added energy and gradients to results to support general use in e.g. energy scans.

* Switched to using the new way to run executables, which supports containers.
* Added an option to just write the input file, without running
Gaussian. This is useful for debugging, and for running Gaussian
on a remote server.

* Fixed a problem with handling the functional if it was a variable rather than a
specific functional.
* Fixed a problem parsing the FChk file. For exponents > 99 the FORTRAN format used
in Gaussian grops the "E", resulting in numbers like 0.947-104 that caused a
problem when trying to read them.