Split software sources - Githubissues

This splits the software documentation into many smaller rst files which are much more manageable, with their own easier to find rendered pages.

Closes #61

Whilst splitting this file into many smaller files, a number of additions and changes were made to the documentation, including:

Adds (basic) documentation for:
- IBM XL compilers (Closes #60)
- Amber (Part of #78)
- EMAN2
- GRACE
- Gromacs (Closes #37, part of #79)
- NAMD
- OpenMM
- PLUMED
- Singularity (Apptainer) (Closes #49)
- Generic python information, with more detailed conda usage (Closes #47)
- nvidia-smi (Closes #75)
- HECBioSim project
- IBM Collaboration project
- Boost Module
- FFTW module
- NVTX library
- PLUMED library
- VTK
- CMake
- Make
Creates new guides section
- Migrates the profiling documentation into the guides section
- Migrates the wanderings about CUDA into the guides section
Adds some notes/warnings about potential WMLCE + RHEL 8 incompatibility. Larger changes still required (#63)
CSS/JS/_templates changes for a useful sidebar with the bootstrap theme with split source files
- New issue #87 opened to consider replacing the theme to an actively maintained theme.
Removes relations.html from the sidebar, as styling issues were difficult to resolve nicely (Closes #77)
Adds sphinxext-rediraffe plugin for redirects for moved .html files (see conf.py)
Assorted RST improvements (links, crossrefs, quoteblocks, code-block, note, etc.)
Clarify module loads for RHEL 7 vs RHEL 8 where appropriate (Part of #73).
Assorted other improvements throughout the documentation

History was a little messy, so has been squashed to avoid .git bloat.

N8-CIR-Bede / documentation