diff --git a/app/src/processing/app/debug/Compiler.java b/app/src/processing/app/debug/Compiler.java
index 285cb7266..e80438433 100644
--- a/app/src/processing/app/debug/Compiler.java
+++ b/app/src/processing/app/debug/Compiler.java
@@ -219,7 +219,7 @@ public class Compiler implements MessageConsumer {
    // collecting them into the core.a library file.
    System.out.println("3. compileCore");
    System.out.println("corePath: " + corePath);
-    compileCore(avrBasePath, buildPath, corePath, pins, pinsPath, configPreferences);
+    compileCore(avrBasePath, buildPath, corePath, systemPath, pins, pinsPath, configPreferences);
 
    
 /*
@@ -762,13 +762,14 @@ public class Compiler implements MessageConsumer {
 	
 	// 3. compile the core, outputting .o files to <buildPath> and then
 	// collecting them into the core.a library file.
-	void compileCore (String avrBasePath, String buildPath, String corePath, String pins, String pinsPath, HashMap<String, String> configPreferences) 
+	void compileCore (String avrBasePath, String buildPath, String corePath, String systemPath, String pins, String pinsPath, HashMap<String, String> configPreferences) 
 		throws RunnerException 
 	{
 		System.out.println("compileCore(...) start");
 
 		ArrayList<String>  includePaths =  new ArrayList();
 	    includePaths.add(corePath); //include core path only
+            includePaths.add(systemPath);
         if (pinsPath != null) includePaths.add(pinsPath);
         
          //debug  includePaths
diff --git a/hardware/sam/cores/sam/Tone.cpp b/hardware/sam/cores/sam/Tone.cpp.xxx
similarity index 100%
rename from hardware/sam/cores/sam/Tone.cpp
rename to hardware/sam/cores/sam/Tone.cpp.xxx
diff --git a/hardware/sam/cores/sam/wiring_analog.c b/hardware/sam/cores/sam/wiring_analog.c.xxx
similarity index 100%
rename from hardware/sam/cores/sam/wiring_analog.c
rename to hardware/sam/cores/sam/wiring_analog.c.xxx
diff --git a/hardware/sam/cores/sam/wiring_pulse.c b/hardware/sam/cores/sam/wiring_pulse.c.xxx
similarity index 100%
rename from hardware/sam/cores/sam/wiring_pulse.c
rename to hardware/sam/cores/sam/wiring_pulse.c.xxx
diff --git a/hardware/sam/system/libsam/include/SAM3S.h b/hardware/sam/system/libsam/include/SAM3S.h
index 1947c6578..fc5405dbe 100644
--- a/hardware/sam/system/libsam/include/SAM3S.h
+++ b/hardware/sam/system/libsam/include/SAM3S.h
@@ -129,7 +129,7 @@ typedef enum IRQn
  * \brief CMSIS includes
  */
 
-#include <core_cm3.h>
+#include <CMSIS/CM3/CoreSupport/core_cm3.h>
 
 /*@}*/
 
diff --git a/hardware/sam/system/libsam/include/acc.h b/hardware/sam/system/libsam/include/acc.h
index 317335448..485b37ca6 100644
--- a/hardware/sam/system/libsam/include/acc.h
+++ b/hardware/sam/system/libsam/include/acc.h
@@ -50,7 +50,7 @@
 /*----------------------------------------------------------------------------
  *        Headers
  *----------------------------------------------------------------------------*/
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 #include <assert.h>
diff --git a/hardware/sam/system/libsam/include/adc.h b/hardware/sam/system/libsam/include/adc.h
index fc7000e38..ebb1ebab6 100644
--- a/hardware/sam/system/libsam/include/adc.h
+++ b/hardware/sam/system/libsam/include/adc.h
@@ -50,7 +50,7 @@
 /*----------------------------------------------------------------------------
  *        Headers
  *----------------------------------------------------------------------------*/
-#include "chip.h"
+#include "../chip.h"
 
 #include <assert.h>
 #include <stdint.h>
diff --git a/hardware/sam/system/libsam/include/crccu.h b/hardware/sam/system/libsam/include/crccu.h
index a49b249ac..bc3d11ed2 100644
--- a/hardware/sam/system/libsam/include/crccu.h
+++ b/hardware/sam/system/libsam/include/crccu.h
@@ -39,7 +39,7 @@
 /*----------------------------------------------------------------------------
  *        Headers
  *----------------------------------------------------------------------------*/
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/dacc.h b/hardware/sam/system/libsam/include/dacc.h
index 5fb280cbe..1458b16ec 100644
--- a/hardware/sam/system/libsam/include/dacc.h
+++ b/hardware/sam/system/libsam/include/dacc.h
@@ -50,7 +50,7 @@
 /*----------------------------------------------------------------------------
  *        Headers
  *----------------------------------------------------------------------------*/
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 #include <assert.h>
diff --git a/hardware/sam/system/libsam/include/efc.h b/hardware/sam/system/libsam/include/efc.h
index faafd477a..8eac6606f 100644
--- a/hardware/sam/system/libsam/include/efc.h
+++ b/hardware/sam/system/libsam/include/efc.h
@@ -53,7 +53,7 @@
 /*----------------------------------------------------------------------------
  *        Headers
  *----------------------------------------------------------------------------*/
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/pio.h b/hardware/sam/system/libsam/include/pio.h
index 29f3473af..f5a588de5 100644
--- a/hardware/sam/system/libsam/include/pio.h
+++ b/hardware/sam/system/libsam/include/pio.h
@@ -5,7 +5,7 @@
  *         Headers
  */
 
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/pwmc.h b/hardware/sam/system/libsam/include/pwmc.h
index 15c9e141c..238d647e6 100644
--- a/hardware/sam/system/libsam/include/pwmc.h
+++ b/hardware/sam/system/libsam/include/pwmc.h
@@ -61,7 +61,7 @@
  *        Headers
  *----------------------------------------------------------------------------*/
 
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/rtc.h b/hardware/sam/system/libsam/include/rtc.h
index 0a5af3fdd..1f4432f5b 100644
--- a/hardware/sam/system/libsam/include/rtc.h
+++ b/hardware/sam/system/libsam/include/rtc.h
@@ -40,7 +40,7 @@
 /*----------------------------------------------------------------------------
  *        Headers
  *----------------------------------------------------------------------------*/
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/rtt.h b/hardware/sam/system/libsam/include/rtt.h
index 6d2b0fdf4..1cbe9740a 100644
--- a/hardware/sam/system/libsam/include/rtt.h
+++ b/hardware/sam/system/libsam/include/rtt.h
@@ -52,7 +52,7 @@
  *        Headers
  *----------------------------------------------------------------------------*/
 
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/spi.h b/hardware/sam/system/libsam/include/spi.h
index a552fe438..3dedf812f 100644
--- a/hardware/sam/system/libsam/include/spi.h
+++ b/hardware/sam/system/libsam/include/spi.h
@@ -41,7 +41,7 @@
  *        Headers
  *----------------------------------------------------------------------------*/
 
-#include "chip.h"
+#include "../chip.h"
 
 /*----------------------------------------------------------------------------
  *        Macros
diff --git a/hardware/sam/system/libsam/include/spi_pdc.h b/hardware/sam/system/libsam/include/spi_pdc.h
index 8a6f755cf..932149700 100644
--- a/hardware/sam/system/libsam/include/spi_pdc.h
+++ b/hardware/sam/system/libsam/include/spi_pdc.h
@@ -40,7 +40,7 @@
 /*----------------------------------------------------------------------------
  *        Headers
  *----------------------------------------------------------------------------*/
-#include "chip.h"
+#include "../chip.h"
 
 /*----------------------------------------------------------------------------
  *        Definitions
diff --git a/hardware/sam/system/libsam/include/ssc.h b/hardware/sam/system/libsam/include/ssc.h
index 722d68f8a..057c90db0 100644
--- a/hardware/sam/system/libsam/include/ssc.h
+++ b/hardware/sam/system/libsam/include/ssc.h
@@ -40,7 +40,7 @@
 /*----------------------------------------------------------------------------
  *        Headers
  *----------------------------------------------------------------------------*/
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/tc.h b/hardware/sam/system/libsam/include/tc.h
index 6bd3a4737..8d4f91a15 100644
--- a/hardware/sam/system/libsam/include/tc.h
+++ b/hardware/sam/system/libsam/include/tc.h
@@ -48,7 +48,7 @@
  *         Headers
  *------------------------------------------------------------------------------*/
 
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/twi.h b/hardware/sam/system/libsam/include/twi.h
index 62e385fcb..561146da8 100644
--- a/hardware/sam/system/libsam/include/twi.h
+++ b/hardware/sam/system/libsam/include/twi.h
@@ -41,7 +41,7 @@
  *         Headers
  *------------------------------------------------------------------------------*/
 
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/twid.h b/hardware/sam/system/libsam/include/twid.h
index 661883c7f..62d20c7a7 100644
--- a/hardware/sam/system/libsam/include/twid.h
+++ b/hardware/sam/system/libsam/include/twid.h
@@ -34,7 +34,7 @@
  *        Headers
  *----------------------------------------------------------------------------*/
 
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/usart.h b/hardware/sam/system/libsam/include/usart.h
index 1dd9e45cc..c4914c0f7 100644
--- a/hardware/sam/system/libsam/include/usart.h
+++ b/hardware/sam/system/libsam/include/usart.h
@@ -58,7 +58,7 @@
  *         Headers
  *------------------------------------------------------------------------------*/
 
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/system/libsam/include/wdt.h b/hardware/sam/system/libsam/include/wdt.h
index 2621754cb..3a0f4341d 100644
--- a/hardware/sam/system/libsam/include/wdt.h
+++ b/hardware/sam/system/libsam/include/wdt.h
@@ -44,7 +44,7 @@
 #ifndef _WDT_
 #define _WDT_
 
-#include "chip.h"
+#include "../chip.h"
 
 #include <stdint.h>
 
diff --git a/hardware/sam/variants/sam3s-ek/variant.h b/hardware/sam/variants/sam3s-ek/variant.h
index 055bffcb1..e42a63166 100644
--- a/hardware/sam/variants/sam3s-ek/variant.h
+++ b/hardware/sam/variants/sam3s-ek/variant.h
@@ -20,6 +20,10 @@
 
 /*----------------------------------------------------------------------------*/
 
+#ifndef sam3s_ek
+#define sam3s_ek
+#endif
+
 /** Name of the board */
 #define VARIANT_NAME "SAM3S-EK"