A brief explanation of branches, through change propagation.

master

This is the upstream - changes are introduced here, and it has some ability to install DUE using the Makefile. It has no Debian specific packaging files.
It also creates the 'upstream tarball' via make orig.tar

debian/master

This is the top level for Debian packaging, and it does have Debian specific packaging files. It is not release specific, but can be used to build DUE as an installable Debian package. See GettingStarted.md for directions for generating a tarfile from the master branch, and building on debian/master

This holds the debian/changelog, and gets updated via 'git merge master'