Look at /etc/ndn/nfd.conf.sample to support NFD ppa
One can either install ndn-cxx, NFD, NLSR, ndn-tools from source or from PPA (apt-get). Currently Mini-NDN does not support those which are installed from PPA.
One potential problem is NLSR from PPA and NLSR from source might have different nlsr.conf file. Since NLSR PPA does not have the nlsr.conf file I am not sure how to get that file - maybe download NLSR - get the git release tag as the one installed in the system and then checkout the nlsr.conf file. Other option is just to ignore this and let users modify ndn/nlsr.py if there is any change in nlsr.conf.
NFD PPA does contain a sample file which can be used.
PS for testing: These two versions cannot exist together and will conflict with each other. So if you are going to install from PPA first remove your versions installed from source (sudo ./waf uninstall). And then when you want to switch back first uninstall PPA (sudo apt-get remove )