change #include "configuration.h" to <helper/configuration.h>

Changes from the flat namespace to heirarchical one.  Instead of writing:

	#include "configuration.h"

the following form should be used.

	#include <helper/configuration.h>

The exception is from .c files in the same directory.

src/ecosboard.c

@@ -24,7 +24,7 @@
 #include "types.h"
 #include "jtag.h"
 #include "ioutil.h"
-#include "configuration.h"
+#include <helper/configuration.h>
 #include "xsvf.h"
 #include "svf.h"
 #include "nand.h"

src/openocd.c

@@ -31,7 +31,7 @@
 #include "openocd.h"
 #include "jtag.h"
 #include "ioutil.h"
-#include "configuration.h"
+#include <helper/configuration.h>
 #include "xsvf.h"
 #include "svf.h"
 #include "nand.h"