References turns into "[? ]" after running thesis.text on Mac

[nayanvs]

Reference [?] issue is solved with the original @kks32 template and works perfectly but, I needed a glossary/abbreviations/nomenclature. So downloaded @clbarnes template. And somehow the issue reappeared. I am surprised that one template has a problem but the other one does not. I would greatly appreciate the help since I am in a rush to catch a thesis deadline.

Originally posted by @nayanvs in #248 (comment)

[clbarnes]

Yes, the original (not to mention the underlying libraries) has seen a lot of updates since my PR was forked. I'll see if my PR can be easily rebased on the current version, but it might not be feasible.

[GR8DAN]

The original template supports nomenclature, see line 132 of thesis.tex.