> ... it insulates the student from the javac command line program, and the command line environment itself
Such a misguided article. The Java language has (quite literally) nothing to do with `javac`. In fact, there's a lot of other compilers out there. Taking a Java class should not focus on the intricacies and weirdness of Java compiler command line interfaces. It seems pretty amateurish to argue in favor of it. Case in point: back in high school, I learned C++ using a Borland compiler (and I haven't touched `bcc` in the 15 years since then, even though I've written plenty of C++ in the meantime).
> ... imports and file naming requirements.
These, again, are (compiler) implementation details and should not be part of a generalized Java curriculum.
> And of course, mathematics is the foundation of computer science.
Stuff like this can be misleading and even though not completely wrong (discrete math, logic, metalogic, mathematical logic are sorta' kinda' similar), it's just wrong enough[1] to lead people astray.
The point of the article is the very concept that the compiler and the Java runtime environment are not the same thing (which an IDE obfuscates to some extent) is what he wants students to learn early on. (And details like that). This leads into a lot of important concepts around how programming languages are seen by the computer.
Learning a programming language has nothing to do with how it's seen by a computer. That's a different class (a class on compilers, maybe). You can even turn Java into Javascript if you want to[1]. The fact that the compilation/transpilation flow here is Java -> Java Bytecode -> JS is meaningless in the context of learning Java.