Command-line Java in AP CS A Context: Over the past school year I spent a significant portion of my time preparing to teach AP CS A next year. From choosing textbooks to writing the College Board syllabus, I essentially started from scratch in designing my course. I'm pleased with all aspects of it as it currently stands, but there is one nagging element: the programming environment.

All students taking AP CS A next year have experience using Cloud9 because that's what we used for C/Python/HTML/CSS this year in AP CSP. Only in the last couple weeks did I discover how easy it is to install the JDK in a Cloud9 workspace and write, compile, and execute programs in Java from the command line. (I had read somewhere a while ago that Java and Cloud9 didn't play nicely.) I had been BlueJ all the way until that point, and I do still very much like BlueJ. However, not having taught the class before, only designed it, here's my (hopefully specific enough) question:

Will students lose anything in their understanding of and proficiency with Java, especially in terms of the AP Exam, if the class only uses a command-line environment for program compilation and execution?

There are many pros/cons to one IDE over another -- a topic which I think is too broad for this community. I just want to make sure, from those who have experience with this course, if there's something that the command-line environment lacks for students that an IDE like BlueJ doesn't lack. I don't want to end up doing students a disservice with respect to the objectives of the course based on this decision.

Edit: Cloud9 is a cloud-based IDE, which makes it ideal for my 1:1 Chromebook environment (however, I do have access to a PC lab for additional software, so that is not a restricting factor for me). As they define it, "Cloud9 combines a powerful online code editor with a full Ubuntu workspace in the cloud." You essentially get a text editor and a terminal for compiling and running programs. I've found that anything I can do via a Linux command line, I can do in Cloud9. It has a number of additional features that make it great for classroom use. I originally chose it because it's the environment used for the CS50 IDE. See more here.
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.