DEF file for Container, and CMake build code

[dcookman]

This PR does two main things:

1. Create a file oxsx_container.def, which can be used to create a Container which holds all of the external dependencies necessary to run OXSX.
2. Add a bunch of CMake files, so that one can compile OXSX within the container.

Some instructions about how to run this has been added to the README.
I also removed a couple of redundant includes in some files, as a cleanup.

[willp240]

This looks cool Daniel! I'm getting an error when trying to build though, probably a my end problem. I think it's because the GLIBC version in the RAT image is not compatible with the one on EL 9. I'll try and play a bit more next week but it might be best if I try and rebuild the RAT container on EL 9 (I said I was going to do that a while back).

In the meantime, I appreciate the tidied headers! And my only minor comment is we could make "Compiling Your Own Scripts" an h2 header in the README so it doesn't look like a subsection of "Alternative Installation Instructions Using Singularity/Apptainer & CMake"