Command-line Java in AP CS A
Similar to @ncmathsadist, I use both command-line environments and IDEs, and I have only found them enhancing each other.  We do most of our work in IDEs, but a few assignments are done in CLIs every year to ensure that students slowly gain some familiarity with those environments.

Reasons for IDEs:


Convenience
Easy integration with GitHub
Error highlighting (though I have some issues with this)
Ease with packages and project integration


Reasons for CLIs:


There are still plenty of important computing platforms (including both iOS and Windows!) that ultimately reduce down to CLIs.
Good luck explaining the string[] args in public static void main(String[] args) if students don't have any experience in CLIs.
Even a little POSIX familiarity goes a long way.