switched from fitpc/atom to prime/linux

Also removed a few old things that had nothing reasonable to be changed
to.
diff --git a/frc971/control_loops/index/index.gyp b/frc971/control_loops/index/index.gyp
index 014f266..dc1c06d 100644
--- a/frc971/control_loops/index/index.gyp
+++ b/frc971/control_loops/index/index.gyp
@@ -60,7 +60,7 @@
         'index_main.cc',
       ],
       'dependencies': [
-        '<(AOS)/atom_code/atom_code.gyp:init',
+        '<(AOS)/linux_code/linux_code.gyp:init',
         'index_lib',
         'index_loop',
       ],
diff --git a/frc971/control_loops/index/index_main.cc b/frc971/control_loops/index/index_main.cc
index c542268..321d74c 100644
--- a/frc971/control_loops/index/index_main.cc
+++ b/frc971/control_loops/index/index_main.cc
@@ -1,6 +1,6 @@
 #include "frc971/control_loops/index/index.h"
 
-#include "aos/atom_code/init.h"
+#include "aos/linux_code/init.h"
 
 int main() {
   ::aos::Init();