Changes from the flat namespace to heirarchical one.  Instead of writing:
	#include "commands.h"
the following form should be used.
	#include <jtag/commands.h>
The exception is from .c files in the same directory.
 #endif
 
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 
 
 #if PARPORT_USE_PPDEV == 1
 
 #endif
 
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 #include <usb.h>
 #include "usb_common.h"
 
 
 
 #include "bitbang.h"
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 
 /**
  * Function bitbang_stableclocks
 
 #ifndef BITQ_H
 #define BITQ_H
 
-#include "commands.h"
+#include <jtag/commands.h>
 
 struct bitq_interface {
        // function to enqueueing low level IO requests
 
 
 /* project specific includes */
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 #include <helper/time_support.h>
 
 #if IS_CYGWIN == 1
 
 #endif
 
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 
 
 #if 1
 
 #endif
 
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 #include "usb_common.h"
 
 
 
 #ifndef MINIDRIVER_IMP_H
 #define MINIDRIVER_IMP_H
 
-#include "commands.h"
+#include <jtag/commands.h>
 
 static inline void interface_jtag_alloc_in_value32(struct scan_field *field)
 {
 
 
 /* project specific includes */
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 #include "rlink.h"
 #include "rlink_st7.h"
 #include "rlink_ep1_cmd.h"
 
 #endif
 
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 #include "usb_common.h"
 
 
 
 #endif
 
 #include "interface.h"
-#include "commands.h"
+#include <jtag/commands.h>
 #include "usb_common.h"
 
 //#define _VSLLINK_IN_DEBUG_MODE_