The odd folder structure is because the original source tree is split into multiple different folders. You can actually download the original source tree from here.
git clone https://usfirst.collab.net/gerrit/allwpilib
I would recommend cloning that, and pushing new updates to that clone if you would like to make changes, that way they are easier to merge.
I know there is some work already being done this summer to try and clean up some of the leftover code from the cRIO, and more help would definitely be appreciated.
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All statements made are my own and not the feelings of any of my affiliated teams.
Teams 1510 and 2898 - Student 2010-2012
Team 4488 - Mentor 2013-2016
Co-developer of
RobotDotNet, a .NET port of the WPILib.