Chap 3 also had references to thesis down and pointed it to the main repo that you forked from. I had never installed Thesisdown before so that through an error for me. After forcing an install of thesisdown, I could get it to knit properly. I removed the references to thesis down and pointed to your own repo. This seems to have resolved the conflict and would allow you README files to build correctly even if a person has never installed thesisdown (this seems ideal, but requires you to make sure that your repo stays up to date).
Chap 3 also had references to thesis down and pointed it to the main repo that you forked from. I had never installed Thesisdown before so that through an error for me. After forcing an install of thesisdown, I could get it to knit properly. I removed the references to thesis down and pointed to your own repo. This seems to have resolved the conflict and would allow you README files to build correctly even if a person has never installed thesisdown (this seems ideal, but requires you to make sure that your repo stays up to date).