When including publications in your thesis there are three sections in the template, 1) Publications include, 2) Submitted manuscripts, and 3) Other publications. I found it hard to work out where to put a publication that was only up on a pre-print server.

The following from Graduate School clarifies what can go where (specifically, it mentions in-prep and rejected manuscripts can go under the "Submitted" section) -

We no longer call it a “thesis by publication”, however, we permit scholarly work to be included in this thesis.

If your work has been published or accepted for publication you should include them under the heading “Publications included in this thesis” and outline the contributions by the authors as shown in the preliminary pages template.

Work that is currently in prep, rejected or under review but part of your Thesis must be included under “Submitted manuscripts included in the thesis”

Work during candidature not included in your Thesis must be acknowledged under “Other publications during candidature”

Authors