There isn't really anything other than training, but they generally don't. You probably can get them to do that with some extra instructions, but part of the problem - at least with Claude - is that it's really trigger-happy about re-running the commands if it doesn't get the results it likes, assuming the results reflects stale results. Even with very expensive (in time) scripts I often see it start a run, pipe it to a file, put it in the background, then loop on sleep statements, occasionally get "frustrated" and check, only to throw the results away 30 seconds after they are done because it's made an unrelated change.

A lot of the time this behaviour is probably right. But it's annoyingly hard to steer it to handle this correctly. I've had it do this even with make targets where the makefile itself makes clear the dependencies means it could trust the cached (in a file) results if it just runs make <target>. Instead I regularly find it reading the Makefile and running the commands manually to work around the dependency management.