$(CORE)_model.exe use to get created in src/ and a symbolic link was
placed in the root mpas directory. This gets confusing on some machines
where the link looks like an executable, but you can't actually copy the
link.

The executable is moved to the MPAS root after it's build rather than
linking it.

Also, the .exe is removed from the executable.

The clean targets were not updated previously to clean the proper files
(${CORE}_model in the root directory).

This commit fixes this issue.

If the makefile sees src/${CORE}_model now at the end of the build, it
will move it to ./${CORE}_model