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1. As a user, I look up a term in the glossary when I encounter it in
the text and do not know what it means, or am not sure what it means in
the context where it appears. If a glossary is focussed on a very
particular subject, I will sometimes read it just to familiarize myself
with the current terminology in that subject area (a glossary of
computer networking terminology for example).
2. I have never written a glossary on the scale you are tackling, but
when I use them, I include words that may appear to be common but in
fact have a very particular meaning in my text (terms such as
"authorized person" or "affected personel" for safety procedures etc.)
and words which are technical in nature, and which an average reader
might not be expected to know (even if your "average reader" is a highly
technical audience--I have often found that people do not retain highly
technical vocabulary even if they have been trained in it unless they
use it every day; thus, you are doing even your sophisticated readers a
favour by clearly defining what you mean by certain techinical terms).
3. Put them in the glossary anyway. The glossary should be complete
according to the guidelines you set up for it. If I know you have a
glossary, I don't want to search the text to look up the definition of a
term if I run across it somewhere other than where it is first defined.