The LWJGL mention was completely accidental, just because I copied and pasted the LWJGL tutorial to create the JOGL tutorial because the process is almost identical. Fixed now!
Thanks.
I went with a directory layout that's slightly different to give the user more freedom- now the architecture part of it is optional, and you can only use the top-level OS directories if you want. This was in response to a user request to be able to ignore the architecture level and only use the OS level, and it seems to work pretty well. I've tried to make the tool as general as possible instead of appealing directly to any one library.
I see what you mean even though I hardly see a case in which you want to ignore the architecture. As long as it's useful for someone, it's cool

The mention of LWJGL is gone (just a copy paste accident!), and the only reason it's on the bottom is because it's the last one I added! I can rearrange it if it's really a big deal, or heck, I could even give each a 50% chance to be on top every time the page is loaded, hahaha.
As you used GlueGen as a source of inspiration and asked us some help, we deserve more than 50% chance

Thanks for taking a look at it, I'm pretty excited to be mentioned on the JOGL site!
You're going to be mentioned in the Wiki as a first step. Then, the other contributors and I will determine whether we should mention your tool directly in the deployment page and in the user guide.
PS- Should I be calling it JOGL or JogAmp? The tutorial only uses JOGL, but I've seen both...
JogAmp includes JOGL, JOAL, JOCL and GlueGen. Use JogAmp where you can, for example when you mean "JOGL and GlueGen". You can add into your tutorial joal.jar and jocl.jar so that our developers won't forget those JARs as well.
PPS- I think I'm keeping the name, but I'll be sure to add what it does in parenthesis or something whenever I introduce it, just like I did in the title here. Hopefully that makes it obvious enough. :p It's already gained some traction on the Processing forum, which I think will be its main use.
As you wish... but it's really confusing.
Edit.: I plan to add something about your tool here:
http://jogamp.org/wiki/index.php/JogAmp_JAR_File_HandlingEdit.2: Please can you fix this spelling mistake? "compile a your game's code" -> "compile your game's code"