As pugixml seems to be well supported nowadays and seems to ship with most distributions it's pretty pointless to keep bundling it with EmulationStation.
CMAKE_INSTALL_PREFIX and CMAKE_INSTALL_DATAROOTDIR are now used to resolve the resource path. As of this commit, there are only two paths where resources are searched, under the user home directory and under this install prefix directory (which defaults to /usr/local/share/emulationstation/resources but can be set to for instance /opt/share/emulationstation/resources using the appropriate CMake flags).