some reorganization: move doc/ to haddock/
reorganize: move manual/ to doc/ (more than just the manual will go there)
update .gitignore [ci skip]
delete outdated stuff from tutorial/ [ci skip]
finish reorganization/cleanup of build system
add a sample equation when explaining MathJax [ci skip]
more work on converting quick start tutorial to ReST format [ci skip]
move tutorial into doc/