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There are several internal variables I use that I do not see a need to document in the user-interface section, but I want to explain in the implementation. I'd really like to remove the warnings about missing references. Can I mark a variable or function as 'not documented' so it won't look for a reference?

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In l3doc, the macro and variable environments takes an optional argument. This can be use to mark the code as

  • aux Auxiliary and so not documented
  • EXP Expandable
  • TF Conditional with T, F and TF versions
  • int Internal code which is documented but not for general use

Thus you want

\begin{variable}[aux]{<name(s)>}

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