This is where I saw the beauty of including dependencies w a project. Even on my own systems, as environments change, things break, and having a stable in-tree reference had paid off.
It's a tough situation, but I find myself leaning to @tedunangst position over the years - usually I try to adapt my machines (incl software) to my needs, but this case I need to take control/responsibility, and here be dragons. Does cmake actually solve this? Do other build systems?