Fellow bookdown enthusiasts,
This is a strange issue. I have a bookdown/Tufte format project. Two days ago in the morning, the 8 rmd file project compiled to pdf fine. I went home for lunch and when I came back, after a couple of small modifications, compilation failed with a number of number of errors I'd never seen before, related to closing $, references not found, indexing-related errors - most or all of which were red herrings. I rolled back the modifications and the project failed to compile. In troubleshooting, I moved the .rmd files to another folder (all of which compile find individually), then brought them back 1 by 1, recompiling each time. Things worked well until I added file #6, which appeared to compile but the resulting pdf file only had 3 of the 6 chapters included. When I added #7, a bunch of errors and compilation failed. It appears that the failure to compile occurs after the .tex file is formed and is being converted to the .pdf. Does anyone know if there's a compilation guide somewhere to help with this? It's a big project and would take days to create a minimal example (I doubt if I even could) so I'm looking for general troubleshooting advice.