Updated .gitignore to include pytest files, and updated table of contents generating logic to ignore directories listed in the .gitignore

Actually added outputs directories to the git repo. Due to the way git tracks files, these directories are only tracked if they contain files, so they now contain .gitignore files so that they're tracked.

Added script to test that all .py scripts in the saltOptimization directory run, and updated ci workflow

A workflow for cloning the dependent repositories and running the tests using pytest.

Removed extraneous symlinks to thermochimia directories, and updated paths in the benchmark and calculation scripts

Need to resolve thermochimica_output path first otherwise the logic that's meant to generate the relative path to the desired output directory will fail

To stop the proliferation of filepaths (that only work on my system with my installation of thermochimica and mstdb-tp) that will ultimately have to be replaced by the end-user (i.e. with the path to their own install of thermochimica and mstdb-tp) all filepaths were made relative to two symlinks to the thermochimica and mstdb-tp directories in the root of the repository, then the only thing that must be changed is the symlink and all of the code in the repo should run without issue

Updated pseduo_binary_calculation function to take absolute paths for the output directory (which makes more sense anyways) and added some logic to automatically convert the absolute output path to a path relative to the thermochimica outputs directory so that the code will run without issue