It seems to me (but I may be wrong) that building the doc requires two runs, like latex: during the first pass, all references are collected and are listed as "undefined" if the anchor has not been encountered yet; it is only during the second run that all references are correctly resolved. It seems that - "sage -docbuild" performs only a single run, so it is not capable to set all the references after a "make doc-clean" - "make doc" performs two passes, thereby resolving all references
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