generalize html compile script

[k-doering-NOAA]

the html compile script includes custom R code to improve formatting. However, some of this code include things like hard coded numbers, which may cause the job to fail with the text of the documentation changes.

It would be great to make this job more robust to issues like this; for example, the section number of references in the table of contents is hard coded; it would be better to figure out this number using the max section number in the manual.