To upgrade Neil, use the following command from within the Neil source tree directory. This directory was created when you cloned Neil repository from https://bitbucket.org/bucket_brigade/neil.
The first command will uninstall Neil from your system. The second one will look for changes on the bitbucket.org server. The third one will update the sources in your source tree to the latest revision. And then you just have to repeat the compilation and installation part all over again.