Many of the files, especially files called index.html, are written by software by doing substitutions in templates. Never edit a file that is machine-generated!. Instead of editing index.html, edit index-template.html and rebuild index.html by running the software.
Most templates are in the same directory as the file that is made from them. But some are in directories one or two levels above that, in cases where templates in sudirectories are all the same. They have names like course-index-template.html or term-index-template.html.