The problem is with the instructions then. So it's an issue in practice only because novices are given bad instructions, without the proper context, that tell t

The problem is with the instructions then. So it's an issue in practice only because novices are given bad instructions, without the proper context, that tell them to do things that are known to be a very bad idea. Similarly, most software used to tell you in the README file to do a "make && make install", sometimes installing into /usr/local but not always. If a user followed these instructions and overwrote half of their distro-provided /usr/lib, things would break in the same way for the same reasons. The solution is to not do that. Don't mix distro-provided files with things installed from other sources. (As for the problem of people providing bad instructions, I don't know the solution. Perhaps remind novices that all instructions come with an implicit context and may not apply fully to their specific case?)