Making documentation when atlaslatex is in texmf
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Note that you cannot simply compile the documentation in the source directory of texmf.

You have to make the following changes:
Remove latex/ in \documentclass and the following \usepackage:
latex/atlaspackage
latex/atlasphysics
latex/atlascontribute
Add option texmf to atlasdoc and atlasphysics
Adapt \graphicspath

Remove bibtex/bst from \bibliographystyle