This creates a new stage called 'Make-doxygen' containing commands to

1. make the doxygen
2. detach from head and delete the local and remote version of gh-pages
3. Remove the history by creating an orphaned gh-pages
4. remove unneccessary folders
5. force an add and commit of the docs folder
6. Use subtree to push the html folder of docs to the the github gh-pages root

Now we can access the docs at mc-stan.org/math

This reverts commit fcfb07f4.