...
git clone ~winger/gem/v_5.1.1/Abs/UQAM_latest/gem
If there were uncommited changes to the code you would like to get as well you will have to copy the modified files by hand. This is not elegant at all, but if you want to make sure you got all modifications you can also remove your source code and then copy the source code you want by hand. For example:
cd ~/gem/v_5.1.1/Abs/My_Abs/gem/src
rm -rf gemdyn modelutils rpnphy
cd ~/gem/v_5.1.1/Abs/My_Abs_directory_to_clone_from/gem/src
rs gemdyn modelutils rpnphy ~/gem/v_5.1.1/Abs/My_Abs/gem/src
c) Create working directories
First change into 'gem' directory that came with the clone:
cd gem
...
~/gem/v_5.1.1/Abs/My_Abs/gem
So the object files, libraries and executables will not be under your home, create links for the directories 'build' and 'work'. Pick a place under which you want to keep the object files, libraries and executables. Preferably under the default(!) space of you professors, for example:
...