There is an empty file ~/.emacs.d/personal.el that you can add personal configuration to.
Changes to personal.el are specifically ignored by Git.
There are several Emacs packages inside conf which have their own particular licences. The scripts unique to emacs-setup are licensed under the GNU Lesser General Public License.
why the LGPL?
The GPL is specifically designed to reduce the usefulness of GPL-licensed code to closed-source, proprietary software. The BSD license (and similar) don't mandate code-sharing if the BSD-licensed code is modified by licensees. The LGPL achieves the best of both worlds: an LGPL-licensed library can be incorporated within closed-source proprietary code, and yet those using an LGPL-licensed library are required to release source code to that library if they change it.