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/keyboard_at.c

@@ -2,21 +2,20 @@
    see COPYING for more details
 */
 #include <stdint.h>
-
 #include "ibm.h"
-#include "disc.h"
-#include "fdc.h"
 #include "io.h"
 #include "mem.h"
 #include "pic.h"
 #include "pit.h"
-#include "sound.h"
-#include "sound_speaker.h"
 #include "timer.h"
-
+#include "disc.h"
+#include "fdc.h"
+#include "sound/sound.h"
+#include "sound/snd_speaker.h"
 #include "keyboard.h"
 #include "keyboard_at.h"
 
+
 #define STAT_PARITY     0x80
 #define STAT_RTIMEOUT   0x40
 #define STAT_TTIMEOUT   0x20