I'm not even sure if I can change that! I don't understand github very well, but as far as I understand, the hydrus site gets automatically generated from a git branch of the hydrus repository called 'gh-pages'. It puts everything under the 'hydrus' directory.
I don't know how to put files in my base user directory. Do you know a way to do that, or to set up a profile page or something like a default redirect to the hydrus repo's pages?