Revamp `figures` documentation

[jaclyn-taroni]

Related to #1176 - here I'm updating the documentation in figures to better reflect the current reality of that directory. I also made a few adjustments to the figure generation shell script based on some issues I identified along the way.

Summary of changes

• Adding sections describing saving individual panels as PDFs to be compiled in Illustrator
• Moved the description of the individual scripts to a README in figures/scripts
• Describing the new disease labels figure palette, including updating the example to reflect the new structure
  • I don't talk about all the columns (e.g., oncoprint_include) but I can if we want
  • Add a note about how the deprecated file is retained
• Reordered some sections and added a TOC to figures/README.md
• Removed the steps for running consensus SNV analyses from figures/generate-figures.sh (the downstream modules use what is in the data release as far as I can tell, so this seems unnecessary)
• Added the breakpoint analysis step (used in the chromothripsis module)

The documentation for the individual figure scripts reflects the changes in #1200

[jaclyn-taroni]

I am going to merge this ahead of #1200 and without CI (docs change only)