By reading writers/latex.py, I found that the cause was referencing
relative HTML url like yade.wrapper.html#yade.wrapper.Sphere (there
were warning about unusable reference target which I overlooked).

I am at loss now as to what is the reference format that will work for
both HTML and LaTeX...

For LaTeX, refuri='#targetName', such as #yade.wrapper.Shape, works
(it is in the same document).

For HTML, this will not work accross file boundary (it creates
hyperlink to anchor named #yade.wrapper.Shape in the _current_ HTML
file, rather than the file that really contains yade.wrapper.Shape
target). The original form mentioning explicitly html filename works,
however.

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