He's referring to the API that lies between the code you write and the system. Regardless of IDE, you still need to import certain basic libraries that provide stuff like I/O and advanced maths.
That said, IDEs are becoming too complex as well. Or rather, they do too much for the programmer. Someone who's learned Java with Eclipse and never had to work on a group project (and even some who have) might have no clue how to compile and run a program outside of that environment. Also, the nature of Autocomplete coerces programmers into writing a program bottom-up, since the IDE can only guess the names of functions already implemented/declared.
IDEs are very useful tools, but everyone should start off with a text editor, a command-line compiler and some version of 'make' before they move onto the time-savers.
Case in point: half of my CompSci group were using Eclipse in 2nd year. After two weeks of committing bad Java code to the repository, they finally asked me how to compile it.
Me: Type 'make'.
Them: We're using Windows.
Me: Yes. Hence the file 'make.bat' in the project dir, alongside the makefile. Just type 'make'.
Them: Why can't you just use Eclipse, like us?
Me: Because I'm buildmaster and it's my job to make sure this works when submitted, at which time it will be tested by someone who does not have Eclipse. And besides, I'm using a basic text editor with syntax highlighting only and I've already done ten times more work than the rest of you put together.
Second-year Computer Science students? :

And people have the damn nerve to complain that the course is
too hard...
But I digress.