Fixed bugs that were preventing NVR and Flash files from behind saved;

A lot of clean ups from waltje;
Start of a directory structure for the code, thanks to waltje.

src/intel.c

@@ -2,14 +2,14 @@
    see COPYING for more details
 */
 #include "ibm.h"
-#include "cpu.h"
+#include "cpu/cpu.h"
 #include "io.h"
 #include "mem.h"
 #include "pit.h"
 #include "timer.h"
-
 #include "intel.h"
 
+
 uint8_t batman_brdconfig(uint16_t port, void *p)
 {
         switch (port)