Follow-up Comment #1, bug #172 (project tex4ht):
I can't confirm the behaviour for \ref{} and \cite{} but only for \footnote{}
and \footcite{}.
In those cases, there is a possibility for a dirty workaround:
$ cat /usr/share/texmf/tex4ht/base/unix/tex4ht.env | sed -E
"s:(4oo.+)(mv):\1sed -E 's/( )\{2,\}(<t4htlink)/\\\\2/g':g" >
~/texmf/tex4ht/base/unix/tex4ht.env && mktexlsr
This changes the "packing" behaviour of "-coo" to not just move the generated
content.xml, but to replace the unwanted whitespaces first. For my usecase
this seems to work. (Make sure the paths are correct and exist on your system
and that you don't override already existing custom settings on your system!)
This workaround is based on some assumptions:
1. The Bug seems to be fixed for \ref and \cite
2. But it is still present for footnotes
3. A single whitespace before a link tag is valid and there because the
TeX-Author wanted it
4. Multiple Spaces are Bug-induced code that is completely unwanted.
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