[Bug] Breaks build system for complex documents

[yardasol]

Describe the bug.

For complex documents, the files in the output/edit folder appear to build just fine, however the files in the output/diff will not build. This version of the output is broken in several ways:

• The script will add a colorbox command to highlight seemingly {\it all} mathematical subscripts. colorbox is not supported in math environments, and for mathematical expression that have many subscripts (i.e. expression in the context of multigroup angle-resolved neutron transport), this results in an unreasonable amount of subscript warnings added.
• The script will add footnotes to section, subsection, subsubsection, etc. titles, which I do not think latex supports.

I'm sure there are others that I have not encountered.

Steps to reproduce the bug.

Steps to reproduce the behavior (ideally as a minimum example of where the failure is coming from with code blocks for error messages and inputs):

1. Checkout the ch3-draft branch of my dissertation.
2. Copy main.tex, chapter3_appendix.tex, chapter3_methods.tex, and figs/ to the input folder
3. Run the w_check.sh script
4. Copy the remaining .tex, bibliography.bib, and uiucthesis2018.cls files to output/edit/ and output/diff/.
5. Run make from within output/edit/ and output/diff/.

What is the expected behavior?

Both collections of documents output to output/edit/ and output/diff/ should build with no errors.

How can this issue be closed?

This issue can be closed when the script can be run and both collections of documents in output/edit/ and output/diff/ build without errors.