Quarto cjm cleanup

[morrowcj]

Summary

Cleanup some of the quarto files

Details

The scientific documentations weren't rendering, due to some errors in the manure.qmd file, so I made a few fixes:

• corrected references to some tables in the manure.qmd file
• renamed some of the manure tables to ensure consistent naming (capitalized acronyms), and updated the references in manure.qmd to match.

Additionally, I took the following steps to clean the repo:

• cleaned up the .gitignore files
• removed preface.qmd, because it was redundant with index.qmd
• renamed the heading for the example_structures.qmd file to "Example quarto structures"
• removed the section numbering from the Preface, Highlighted Updates, and Example quarto structures
• removed the intermediate jupyter notebook file "quarto_ipynb_1".
• removed the pdf setting from the quarto configuration file (_quarto.yml), since we've decided to prioritize having a PDF
• moved quarto_audit.py to scripts, where it more naturally belongs. I also modified the script so that it works from this new directory (with python scripts/quarto_audit.py from the quarto-scidoc directory).
• moved the abbrevs.qmd file to the qmd directory, updating the code to work properly from the new location
• updated the readme file to reflect the relevant changes.

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Some additional things that I noticed that I did not change, because I didn't know what steps to take:

• Table 2.30 in manure.qmd (tbl-mn-cp-met-conv) doesn't render properly, likely because of the dual-headings the table has and the > symbol.
• Table 2.29 and 2.30 in manure.qmd (tbl-mn-cp-met-conv and tbl-mn-cp-inputs) have the same caption.

[morrowcj]

@LisaM-kiwi, when you get a chance (after your trip), could you review these changes? I'll make a separate PR with my actual SC documentation review.

[LisaM-kiwi]

@LisaM-kiwi, when you get a chance (after your trip), could you review these changes? I'll make a separate PR with my actual SC documentation review.

Thanks @morrowcj! I'll go and try to figure out the additional things you mentioned on your branch and then I'll merge them with the changes you made.

[LisaM-kiwi]

@morrowcj I went in and updated the caption for Table 2.30 and I edited it to make it render better. It's not as good as I would like, the main issue is I can't figure out how to change the column width so the last column is crunched. This is a problem in multiple places. I've tried a few fixes but I haven't been able to get any to work.

I still need to look into the merge conflict to see what the issue is there.