As I understand them
canonical URLs distinguish between the same content accessed through different URL forms. Currently Google thinks the documentation is mostly located at
www.sagemath.org/doc/ while we want it to appear at
doc.sagemath.org/html/en, so the canonical links should help with that distinction. It's unclear to me that it will have any effect on
combinat.sagemath.org/doc/, since that is much older content and Google should be able to tell the difference.
The biggest problem right now, however, is that Google is taking a very long time to index
doc.sagemath.org at all. At the beginning of June I created sitemaps listing every HTML and PDF document in the Sage documentation and Harald submitted them to Google promptly. After about a month most of the PDF links were indexed and those documents appear at the new location. At about the same time less than a third of the HTML links were listed as indexed by Google. That figure has been steady for the last month, and is currently just a bit over one third.
In order to prompt Google to index the sitemap, over the last month I have manually removed links to documents at
www.sagemath.org/doc/ in Google's webmaster tools and added them to the index at
doc.sagemath.org/html/en. This has had little effect: even links I've added manually several times still will not appear in a search including site:
doc.sagemath.org. Google is just taking it's time to index the new location, even with an explicit sitemap of all HTML files.
If someone knows a better way to prompt Google to index a sitemap I'm all ears, but I don't think it's possible. If we want the documentation to appear at
doc.sagemath.org we simply need to wait until Google indexes things. Adding canonical links isn't likely to have an effect if the documents aren't getting indexed.
Regarding
combinat.sagemath.org/doc/ I don't think removing it is a displacement of the problem. This is the only other copy of the documentation in the
sagemath.org domain. Presumably Google thinks it's relevant even though old because it is located in the same /doc/ directory where Google thinks the newer documentation is located. Removing it from the Internet and pointing to the newer version at
doc.sagemath.org would be in the best interest of the entire Sage community, if anyone knows who has access to it.
TL;DR waiting for Google to index...