I've been browsing the lwjgl 3 github page and I can't find where the actual native files for the modules are found. Does lwjgl store it on github somewhere or does it download them from a the module's website when it makes a new build?
You can obtain a working distribution of LWJGL3 from either the GitHub Releases site: https://github.com/LWJGL/lwjgl3/releases
or from the lwjgl.org download site: https://www.lwjgl.org/download
The sources repository of LWJGL3 contains neither the natives nor all java classes necessary to use LWJGL3, because most of it is generated during the build process.
Thanks for your help. Is there a resource I can view to see how the natives are built?
The natives for most modules are built together with the rest of LWJGL. You can find the Ant scripts here (https://github.com/LWJGL/lwjgl3/tree/master/config), see the <platform>/build.xml files.
Modules that are too big to include in the LWJGL repository or have complicated build procedures, are built on our continuous integration solutions (Travis-CI (https://travis-ci.org/) for Linux and macOS and a private Amazon EC2 server for Windows). The source for those builds can be found in the LWJGL-CI (https://github.com/LWJGL-CI?tab=repositories) account. Each repository has two branches, one for Linux and one for macOS. In each branch there's a .travis.yml script that describes the corresponding build. The Linux branch is also used by our TeamCity server (http://teamcity.lwjgl.org/) to do the Windows builds (the build steps are very similar). Any LWJGL-specific changes to these repositories are continuously rebased on top of the upstream branches, when synchronized. Some are synchronized automatically on each upstream change (Assimp & GLFW), others are synchronized manually (bgfx, jemalloc, OpenAL-Soft).