% !TEX root = John11-w.tex
% John11-w.tex

\input{_header}           % loads comment package, excludes glossarytext by default

\definingfootnotestrue
\input{_glossary}         % pass 1: \ifdefiningfootnotes true, glossarytext excluded

\begin{document}
\input{_BiblioRef}
\input{John11}

\includecomment{glossarytext}
\definingfootnotesfalse
\input{_glossary}         % pass 2: \ifdefiningfootnotes false, glossarytext included

\end{document}