Update docs to 4.1.0

[mikix]

Here's what I did to generate these:

• git checkout v4.1.0
• installed doxygen and doxypypy per README.md
• ran doxygen -u to update the config
• manually edited Doxyfile to set the correct version (4.1.0)
• ran PATH=$PATH:. doxygen (because otherwise it wouldn't find ./Doxyfilter and generate class info)
• Deleted all contents of gh-pages branch, copied docs/html over into it, and git added everything.

I think github is hooked up so that updates to this branch will go live automatically. If not, we can investigate once the files are updated at least.

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