Change to use a Python3 module structure from the start

There's a lot of difficulty for students to share their agents
between each other. When they start the project they don't think about
the need to make it into a module since it "runs".

A lot has been done in this commit, move everything to a separate folder
which the students have to rename. Reformat the README.md to respect
people reading it in the terminal and add some more instructions for the
setup.