I have not been able to find a reason for this. Is there a log of what 
Sphinx is doing when it assigns footnote numbers? 

After I updated to Sphinx 1.7.1, I noticed an additional symptom - it not 
only skips numbers in the beginning, but also skips numbers between most 
chapters. That is, Ch.1 includes footnotes numbered 32-36, then Ch. 2 
starts at footnote 51 and goes to 65. 

There is one place in my document where it doesn't skip numbers between 
chapters - Ch. 4 has footnotes 104-105 and Ch. 5 has footnotes 106-107. 
Then Ch. 6 has 123-126 so it's back to skipping numbers. Ch. 4 and Ch. 5 do 
not have any subheads - they only have one level per chapter. 

If I get a chance to mock up a project I will see if I can test that 
question about subheadings being related to the footnote numbering issue; I 
can't share my actual files publicly and they're a bit complicated. 

I do get error messages about _all_ of the footnotes when I build - 
including the ones that don't show up in the document - but I think that 
the error messages are not related to this problem. (Similar to this 
case: https://tex.stackexchange.com/questions/16268/ ) So it seems that the 
document thinks there's a footnote 1, it just doesn't appear in the final 
document. 

pdfTeX warning (dest): name{Hfootnote.3} has been referenced but does not 
exist
, replaced by a fixed one

pdfTeX warning (dest): name{Hfootnote.2} has been referenced but does not 
exist
, replaced by a fixed one

pdfTeX warning (dest): name{Hfootnote.1} has been referenced but does not 
exist
, replaced by a fixed one

I looked at the strategies mentioned in this thread 
https://github.com/sphinx-doc/sphinx/issues/3652 for forcing numbers to 
restart at each chapter, but I didn't get any of them to work. Resetting 
the numbers at the beginning of each chapter would be an acceptable 
workaround. 


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