LaTeX.org

Thank you, Ijon
That fixed the issue by just replacing \usepackage{makeidx} with \usepackage{imakeidx} in my packages.tex file and then recompiling (twice) main.tex.

I am trying to create a simple index at the end of my main.pdf document. I am using TeXStudio for the compile. I created a user command (Options/Configure TeXStudio/Build).

name: user0:Make Nomenclature
command: makeindex %.nlo -t %.nlg -o %.nls

When I run the command using Tools/User/Make ...