URET Android Reverser Toolkit v1.1

[Mkz]

Dex2Jar (hxxps://github.com/pxb1988/dex2jar/releases) will do what you want, it writes the converted classes from the source .dex directly into the .jar, bypassing the case insensitivity limitation of the Windows FS.
I just tried it on an apk/dex I had here and the resulting .jar did contain a.class and A.class in the same folder. jd-gui was able to decompile each of them separately.

Note that you can also use Dex2Jar to convert a .jar to .dex, so that you can analyze it under JEB.
One of the best features I like about JEB is the fact that it lets you rename each class/type and variable names to something meaningful as you interpret the logic, and it will replace every reference to it (excepty reflection or string literals, of course). I don't remember any other tool that allows that.
The problem with JEB is that it's rather unstable and some classes or methods make it crash, not all methods can be decompiled, etc. But I guess most Java decompilers have that problem too.