Hi Mohamed,
Zapdos includes MOOSE as a submodule, so that a version of MOOSE that is guaranteed to work with the current version of Zapdos is always available. Thats why the Zapdos instructions include initializing submodules. The instructions do not include needing to build libmesh inside of that submodule, though, so we probably need to add that.
Try this: navigate to the Zapdos folder, then run:
- cd moose
- scripts/update_and_build_libmesh.sh
This will build libmesh as before, but specifically for the version of MOOSE within the submodule in Zapdos. Then, you can try make on Zapdos again to build and test it. Let me know if that helps!
Casey