Describe the issue linked to the documentation

Right now, references are scattered around the User Guide as needed for different sections. and not all articles cited are present in the bibtex file. This issue piggybacks on #1048 and #1056.

Suggest a potential alternative/fix

Someone should look through the User Guide and aggregate all missing references into the refs.bib file, and then replace references throughout with the new citation style. This fix was also suggested by @MiroDudik in PR #1032, which has good guidance for implementation.