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that's right. It's a bit weird how make gh-pages works, in that you run it from one repo (the one this issue is on) but it also creates commits in another repo (ipython.github.com - the one we serve, which is called gh-pages locally). The problem is that the way this currently happens, we just wholesale copy everything in this repos directory (whether or not it is checked into git), and check it into the gh-pages repo.
I don't think we should need a separate command to add a file to the website - that's common enough (for images etc.) that I want it to be simple.
As I see it, the second git repository is just an implementation detail - the process to upload the built website happens to be pushing it to a git repository, but the make target would work the same way if it were using rsync, say.
If things are getting uploaded incorrectly, I think the point to address that is the build process which puts them into the destination folder. Once they're in there, they're fair game for uploading.
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