> instead of just telling them to use the tools you can teach students how to use them well
Yes, that would be great. If only I'd ever met a teacher able and motivated enough to do that. Coincidentally, it's easier to teach about how to run a couple CLI commands and read the documentation than explaining a behemoth including everything from version control to debuggers that's all thrown in your face at once.
Hmm, what would the lesson look like? I doubt there is a way to teach everything about out-of-IDE/advanced Java development in just a single hour or two. You mentioned CLASSPATH, but there are also JARs with manifest files, there are multitude of build systems with their own configuration languages/plugins/conventions, there are ClassLoaders, there are Java Compiler Plugins... Just too much.
You either list terms for two hours straight without any details and exercises or you choose some semi-random subset of topics, which may very well not include CLASSPATH for some reason. Alternatively, you teach for ten hours instead of two.
This part stays intact either way though. You're not wrong that teaching students to run a couple of CLI commands is easier, but they still need to understand what they're doing, otherwise it can be just about as opaque as clicking a button in a graphical program.
Considering the vast majority of them will be using IDEs if they are coding in Java professionally, personally I feel it is worth taking some extra time to at least give them a starting-off point and then letting them access the documentation that the IDEs themselves provide. Whether this comes after teaching them the basics of the language through the barebones text editor + CLI tools approach or is what they are taught from the ground up is a matter of choice.
This is fixable though, instead of just telling them to use the tools you can teach students how to use them well. It also doesn't hurt to inculcate a mindset that shows them how to look for help when they are stuck. Discarding the IDE entirely is like throwing the baby out with the bathwater in my opinion.