This answer is going to briefly explain how the native files are handled on the latest launcher.
As of 4/29/2017 the Minecraft launcher for Windows extracts all native files and places them info %APPDATA%\Local\Temp{random folder}. That folder is temporary and is deleted once the javaw.exe process finishes (when Minecraft is closed). The location of that temporary folder must be provided in the launch arguments as the value of
-Djava.library.path=
Also, the latest launcher (2.0.847) does not show you the launch arguments so if you need to check them yourself you can do so under the Task Manager (simply enable the Command Line tab and expand it) or by using the WMIC
utility as explained here.
Hope this helps some people who are still interested in doing this in 2017.