To setup wowengine with upt just install upt with npm ( Nodejs is required to run npm and upt ):
npm install -g upt
and then run
upt install wowengine/game#3.3.5a
if you want to test the compiling, just run from the same folder
mkdir build
cd build
cmake ../upt-modules/wowengine/src/game/3.3.5a -DPREFIX=/home/$USER/wowengine-server
make
To compile you need the requirements specified in trinitycore project: http://collab.kpsn.org/display/tc/TrinityCore+Requirements
You can also compile only core libraries using these commands from root folder:
mkdir build
cd build
cmake ../upt-modules/hw2/modules/c++/src/project
make