diff --git a/.gitignore b/.gitignore
index 0ff1ebfa2..c80b86fd0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,7 +12,7 @@
 *.ihex
 *.pyc
 *~
-obj_*
+build/*
 Makefile.target
 Makefile.*.defines
 tools/doxygen/html
diff --git a/Makefile.include b/Makefile.include
index a194274bd..672c7f4c1 100644
--- a/Makefile.include
+++ b/Makefile.include
@@ -13,8 +13,6 @@ include $(CONTIKI)/Makefile.identify-target
 ### Include Makefile.tools to pull in targets that allow us to build tools dir
 include $(CONTIKI)/Makefile.tools
 
-CONTIKI_NG_TARGET_LIB = contiki-ng-$(TARGET).a
-
 ifeq ($(DEFINES),)
   -include Makefile.$(TARGET).defines
   ifneq ($(DEFINES),)
@@ -39,7 +37,12 @@ ifdef CI
   endif
 endif
 
-OBJECTDIR = obj_$(TARGET)
+BUILD_DIR = build
+BUILD_DIR_TARGET = $(BUILD_DIR)/$(TARGET)
+BUILD_DIR_BOARD = $(BUILD_DIR_TARGET)/$(BOARD)/$(BUILD_DIR_CONFIG)
+OBJECTDIR = $(BUILD_DIR_BOARD)/obj
+
+CONTIKI_NG_TARGET_LIB = $(BUILD_DIR_BOARD)/contiki-ng-$(TARGET).a
 
 LOWERCASE = -abcdefghijklmnopqrstuvwxyz/
 UPPERCASE = _ABCDEFGHIJKLMNOPQRSTUVWXYZ_
@@ -75,10 +78,6 @@ endef
 CONTIKI_OBJECTFILES = ${addprefix $(OBJECTDIR)/,${call oname, $(CONTIKI_SOURCEFILES)}}
 PROJECT_OBJECTFILES = ${addprefix $(OBJECTDIR)/,${call oname, $(PROJECT_SOURCEFILES)}}
 
-# Provide way to create $(OBJECTDIR) if it has been removed by make clean
-$(OBJECTDIR):
-	mkdir $@
-
 uniq = $(if $1,$(firstword $1) $(call uniq,$(filter-out $(firstword $1),$1)))
 
 ### Include target makefile (TODO Unsafe?)
@@ -124,6 +123,11 @@ endif # $(BOARD) not empty
 
 PLATFORM_ACTION ?= build
 
+# Provide way to create $(OBJECTDIR) if it has been removed by make clean
+$(OBJECTDIR):
+	$(TRACE_MKDIR)
+	$(Q)mkdir -p $@
+
 ifneq ($(BOARD),)
   TARGET_BOARD_UPPERCASE := ${strip ${shell echo $(BOARD) | sed y!$(LOWERCASE)!$(UPPERCASE)!}}
   CFLAGS += -DCONTIKI_BOARD_$(TARGET_BOARD_UPPERCASE)=1
@@ -241,12 +245,20 @@ ifeq ($(V),1)
   TRACE_LD =
   TRACE_AR =
   TRACE_AS =
+  TRACE_OBJCOPY  =
+  TRACE_OBJDUMP  =
+  TRACE_MKDIR =
+  TRACE_CP =
   Q=
 else
   TRACE_CC = @echo "  CC       " $<
   TRACE_LD = @echo "  LD       " $@
   TRACE_AR = @echo "  AR       " $@
   TRACE_AS = @echo "  AS       " $<
+  TRACE_OBJCOPY  = @echo "  OBJCOPY  " $< "-->" $@
+  TRACE_OBJDUMP  = @echo "  OBJDUMP  " $< "-->" $@
+  TRACE_MKDIR = @echo "  MKDIR    " $@
+  TRACE_CP       = @echo "  CP       " $< "-->" $@
   Q=@
 endif
 
@@ -303,14 +315,13 @@ endef
 
 ### Harmonize filename of a .map file, if the platform's build system wants
 ### to create one
-CONTIKI_NG_PROJECT_MAP = $(addsuffix -$(TARGET).map, $(basename $@))
+CONTIKI_NG_PROJECT_MAP = $(BUILD_DIR_BOARD)/$(basename $(notdir $@)).map
 
 .PHONY: clean distclean usage help targets boards savetarget savedefines viewconf
 
 clean:
-	-$(Q)rm -f *.d *.e *.o $(CONTIKI_NG_TARGET_LIB) $(CLEAN)
-	-$(Q)rm -rf $(OBJECTDIR)
-	-$(Q)rm -f $(addsuffix -$(TARGET).map, $(CONTIKI_PROJECT))
+	-$(Q)rm -f *.d *.e *.o $(CLEAN)
+	-$(Q)rm -rf $(BUILD_DIR_TARGET)
 	-$(Q)rm -f $(addsuffix .$(TARGET), $(CONTIKI_PROJECT))
 	@echo Target $(TARGET) cleaned
 
@@ -319,6 +330,7 @@ distclean:
 		echo Running: $(MAKE) TARGET=$$TARG clean; \
 		$(MAKE) TARGET=$$TARG clean; \
 	done
+	-$(Q)rm -rf $(BUILD_DIR)
 
 -include $(CONTIKI)/arch/platform/$(TARGET)/Makefile.customrules-$(TARGET)
 
@@ -383,12 +395,16 @@ ifndef LD
 endif
 
 ifndef CUSTOM_RULE_LINK
-%.$(TARGET): %.o $(PROJECT_OBJECTFILES) $(PROJECT_LIBRARIES) $(CONTIKI_NG_TARGET_LIB)
+$(BUILD_DIR_BOARD)/%.$(TARGET): %.o $(PROJECT_OBJECTFILES) $(PROJECT_LIBRARIES) $(CONTIKI_NG_TARGET_LIB)
 	$(TRACE_LD)
 	$(Q)$(LD) $(LDFLAGS) $(TARGET_STARTFILES) ${filter-out %.a,$^} \
 	    ${filter %.a,$^} $(TARGET_LIBFILES) -o $@
 endif
 
+%.$(TARGET): $(BUILD_DIR_BOARD)/%.$(TARGET)
+	$(TRACE_CP)
+	$(Q)cp $< $@
+
 %.ramprof: %.$(TARGET)
 	$(NM) -S -td --size-sort $< | grep -i " [abdrw] " | cut -d' ' -f2,4
 
@@ -446,9 +462,9 @@ ifeq ($(findstring $(TARGET),native cooja),)
   include $(CONTIKI)/Makefile.embedded
 endif
 
-# Don't treat %.$(TARGET) as an intermediate file because it is
-# in fact the primary target.
-.PRECIOUS: %.$(TARGET)
+# Don't treat $(BUILD_DIR_BOARD)/%.$(TARGET) and $(TARGET) as intermediate
+# files because for many platforms they are in fact the primary target.
+.PRECIOUS: $(BUILD_DIR_BOARD)/%.$(TARGET) %.$(TARGET)
 
 # Cancel the predefined implict rule for compiling and linking
 # a single C source into a binary to force GNU make to consider
diff --git a/arch/cpu/arm/Makefile.arm b/arch/cpu/arm/Makefile.arm
index 83f9b8a36..e8befdb86 100644
--- a/arch/cpu/arm/Makefile.arm
+++ b/arch/cpu/arm/Makefile.arm
@@ -1,3 +1,11 @@
+### Verbosity control. Use  make V=1 to get verbose builds.
+### Extends what we already have in the top-level Makefile
+ifeq ($(V),1)
+  TRACE_SREC_CAT =
+else
+  TRACE_SREC_CAT = @echo "  SREC_CAT " $< "-->" $@
+endif
+
 CC       = arm-none-eabi-gcc
 CPP      = arm-none-eabi-cpp
 LD       = arm-none-eabi-gcc
@@ -43,22 +51,32 @@ endif
 ### CPU-dependent cleanup files
 CLEAN += *.elf *.bin *.lst *.hex *.i16hex
 
+OUT_HEX = $(BUILD_DIR_BOARD)/%.hex
+OUT_I16HEX = $(BUILD_DIR_BOARD)/%.i16hex
+OUT_BIN = $(BUILD_DIR_BOARD)/%.bin
+OUT_LST = $(BUILD_DIR_BOARD)/%.lst
+
 ### Don't treat the following files as intermediate
-.PRECIOUS: %.elf %.hex %.bin
+.PRECIOUS: $(OUT_ELF) $(OUT_HEX) $(OUT_BIN)
 
-%.i16hex: %.elf
-	$(OBJCOPY) -O ihex $< $@
+$(OUT_I16HEX): $(OUT_ELF)
+	$(TRACE_OBJCOPY)
+	$(Q)$(OBJCOPY) -O ihex $< $@
 
-%.hex: %.i16hex
-	$(SREC_CAT) $< -intel -o $@ -intel
+$(OUT_HEX): $(OUT_I16HEX)
+	$(TRACE_SREC_CAT)
+	$(Q)$(SREC_CAT) $< -intel -o $@ -intel
 
-%.bin: %.elf
-	$(OBJCOPY) -O binary $(OBJCOPY_FLAGS) $< $@
+$(OUT_BIN): $(OUT_ELF)
+	$(TRACE_OBJCOPY)
+	$(Q)$(OBJCOPY) -O binary $(OBJCOPY_FLAGS) $< $@
 
-%.lst: %.elf
-	$(OBJDUMP) $(OBJDUMP_FLAGS) $< > $@
+$(OUT_LST): $(OUT_ELF)
+	$(TRACE_OBJDUMP)
+	$(Q)$(OBJDUMP) $(OBJDUMP_FLAGS) $< > $@
 
 ### We don't really need the .hex and .bin for the .$(TARGET) but let's make
 ### sure they get built
-%.$(TARGET): %.elf %.hex %.bin
-	cp $< $@
+$(BUILD_DIR_BOARD)/%.$(TARGET): $(OUT_ELF) $(OUT_HEX) $(OUT_BIN)
+	$(TRACE_CP)
+	$(Q)cp $< $@
diff --git a/arch/cpu/arm/cortex-m/Makefile.cortex-m b/arch/cpu/arm/cortex-m/Makefile.cortex-m
index aebcf2bdd..0ca1d54ff 100644
--- a/arch/cpu/arm/cortex-m/Makefile.cortex-m
+++ b/arch/cpu/arm/cortex-m/Makefile.cortex-m
@@ -3,11 +3,25 @@ CONTIKI_ARM_DIRS += cortex-m cortex-m/CMSIS
 ### Build syscalls for newlib
 MODULES += os/lib/newlib
 
+LDFLAGS += -T $(LDSCRIPT)
+LDFLAGS += -Wl,--gc-sections,--sort-section=alignment
+LDFLAGS += -Wl,-Map=$(CONTIKI_NG_PROJECT_MAP),--cref,--no-warn-mismatch
+
+OBJCOPY_FLAGS += --gap-fill 0xff
+
+CPU_STARTFILES = ${addprefix $(OBJECTDIR)/,${call oname, $(CPU_START_SOURCEFILES)}}
+
+### Resolve any potential circular dependencies between the linked libraries
+### See: https://stackoverflow.com/questions/5651869/gcc-what-are-the-start-group-and-end-group-command-line-options/5651895
+TARGET_LIBFLAGS := -Wl,--start-group $(TARGET_LIBFILES) -Wl,--end-group
+
 CUSTOM_RULE_LINK = 1
 
+OUT_ELF = $(BUILD_DIR_BOARD)/%.elf
+
 .SECONDEXPANSION:
 
-%.elf: $(CPU_STARTFILES) $$(CONTIKI_OBJECTFILES) %.o $(PROJECT_OBJECTFILES) $(PROJECT_LIBRARIES) $(LDSCRIPT) $(TARGET_LIBS)
+$(OUT_ELF): $(CPU_STARTFILES) $$(CONTIKI_OBJECTFILES) %.o $(PROJECT_OBJECTFILES) $(PROJECT_LIBRARIES) $(LDSCRIPT) $(TARGET_LIBS)
 	$(TRACE_LD)
 	$(Q)$(LD) $(LDFLAGS) ${filter-out $(LDSCRIPT) %.a,$^} ${filter %.a,$^} $(TARGET_LIBFLAGS) -o $@
 
diff --git a/arch/cpu/arm/cortex-m/cm3/Makefile.cm3 b/arch/cpu/arm/cortex-m/cm3/Makefile.cm3
index 3cf216bfb..b4bf612da 100644
--- a/arch/cpu/arm/cortex-m/cm3/Makefile.cm3
+++ b/arch/cpu/arm/cortex-m/cm3/Makefile.cm3
@@ -3,16 +3,7 @@ CONTIKI_ARM_DIRS += cortex-m/cm3
 CFLAGS += -mcpu=cortex-m3
 
 LDFLAGS += -mcpu=cortex-m3 -nostartfiles
-LDFLAGS += -T $(LDSCRIPT)
-LDFLAGS += -Wl,--gc-sections,--sort-section=alignment
-LDFLAGS += -Wl,-Map=$(CONTIKI_NG_PROJECT_MAP),--cref,--no-warn-mismatch
 
-OBJCOPY_FLAGS += --gap-fill 0xff
-
-CPU_STARTFILES = ${addprefix $(OBJECTDIR)/,${call oname, $(CPU_START_SOURCEFILES)}}
-
-### Resolve any potential circular dependencies between the linked libraries
-### See: https://stackoverflow.com/questions/5651869/gcc-what-are-the-start-group-and-end-group-command-line-options/5651895
-TARGET_LIBFLAGS := -Wl,--start-group $(TARGET_LIBFILES) -lm -Wl,--end-group
+TARGET_LIBFILES += -lm
 
 include $(CONTIKI)/arch/cpu/arm/cortex-m/Makefile.cortex-m
diff --git a/arch/cpu/arm/cortex-m/cm4/Makefile.cm4 b/arch/cpu/arm/cortex-m/cm4/Makefile.cm4
index b0b592e43..7443681ea 100644
--- a/arch/cpu/arm/cortex-m/cm4/Makefile.cm4
+++ b/arch/cpu/arm/cortex-m/cm4/Makefile.cm4
@@ -3,16 +3,5 @@ CONTIKI_ARM_DIRS += cortex-m/cm4
 CFLAGS += -mcpu=cortex-m4
 
 LDFLAGS += -mcpu=cortex-m4
-LDFLAGS += -T $(LDSCRIPT)
-LDFLAGS += -Wl,--gc-sections,--sort-section=alignment
-LDFLAGS += -Wl,-Map=$(CONTIKI_NG_PROJECT_MAP),--cref,--no-warn-mismatch
-
-OBJCOPY_FLAGS += --gap-fill 0xff
-
-CPU_STARTFILES = ${addprefix $(OBJECTDIR)/,${call oname, $(CPU_START_SOURCEFILES)}}
-
-### Resolve any potential circular dependencies between the linked libraries
-### See: https://stackoverflow.com/questions/5651869/gcc-what-are-the-start-group-and-end-group-command-line-options/5651895
-TARGET_LIBFLAGS := -Wl,--start-group $(TARGET_LIBFILES) -Wl,--end-group
 
 include $(CONTIKI)/arch/cpu/arm/cortex-m/Makefile.cortex-m
diff --git a/arch/cpu/cc26xx-cc13xx/Makefile.cc26xx-cc13xx b/arch/cpu/cc26xx-cc13xx/Makefile.cc26xx-cc13xx
index 592ddfbd8..94f4e5111 100644
--- a/arch/cpu/cc26xx-cc13xx/Makefile.cc26xx-cc13xx
+++ b/arch/cpu/cc26xx-cc13xx/Makefile.cc26xx-cc13xx
@@ -81,8 +81,10 @@ STACK_SIZE = 0
 	@$(SIZE) -A $< | egrep "data|bss" | awk '{s+=$$2} END {s=s+$(STACK_SIZE); f=$(RAM_SIZE)-s; printf "[RAM]   used %6d, free %6d\n",s,f;}'
 	@$(SIZE) -A $< | egrep "text|isr_vector" | awk '{s+=$$2} END {f=$(FLASH_SIZE)-s; printf "[Flash] used %6d, free %6d\n",s,f;}'
 
+include $(CONTIKI)/arch/cpu/arm/cortex-m/cm3/Makefile.cm3
+
 ifeq ($(BOARD_SUPPORTS_BSL),1)
-%.upload: %.bin
+%.upload: $(OUT_BIN)
 ifeq ($(wildcard $(BSL)), )
 	@echo "ERROR: Could not find the cc2538-bsl script. Did you run 'git submodule update --init' ?"
 else
@@ -95,5 +97,3 @@ endif
 
 ### For the login etc targets
 BAUDRATE = 115200
-
-include $(CONTIKI)/arch/cpu/arm/cortex-m/cm3/Makefile.cm3
diff --git a/arch/cpu/nrf52832/Makefile.nrf52832 b/arch/cpu/nrf52832/Makefile.nrf52832
index c97c728e5..098033ce4 100644
--- a/arch/cpu/nrf52832/Makefile.nrf52832
+++ b/arch/cpu/nrf52832/Makefile.nrf52832
@@ -172,11 +172,11 @@ vpath %.s $(ASM_PATHS)
 
 OBJECTS = $(C_OBJECTS) $(ASM_OBJECTS)
 
-CLEAN += nrf52832.a
+NRFLIB = $(BUILD_DIR_BOARD)/nrf52832.a
 
-TARGET_LIBS = nrf52832.a $(NRF52_SDK_ROOT)/components/iot/ble_6lowpan/lib/ble_6lowpan.a
+TARGET_LIBS = $(NRFLIB) $(NRF52_SDK_ROOT)/components/iot/ble_6lowpan/lib/ble_6lowpan.a
 
-nrf52832.a: $(OBJECTS)
+$(NRFLIB): $(OBJECTS)
 	$(TRACE_AR)
 	$(Q)$(AR) $(AROPTS) $@ $^
 
diff --git a/arch/platform/cc2538dk/Makefile.cc2538dk b/arch/platform/cc2538dk/Makefile.cc2538dk
index d80fd8d5f..148c6e837 100644
--- a/arch/platform/cc2538dk/Makefile.cc2538dk
+++ b/arch/platform/cc2538dk/Makefile.cc2538dk
@@ -28,11 +28,12 @@ endif
 
 BSL = $(CONTIKI)/tools/cc2538-bsl/cc2538-bsl.py
 
-%.upload: %.bin %.elf
+%.upload: $(OUT_BIN) $(OUT_ELF)
 ifeq ($(wildcard $(BSL)), )
 	@echo "ERROR: Could not find the cc2538-bsl script. Did you run 'git submodule update --init' ?"
 else
-	$(eval BSL_ADDRESS_ARG := -a $(shell $(OBJDUMP) -h $*.elf | grep -B1 LOAD | \
+	$(eval BSL_ADDRESS_ARG := -a $(shell $(OBJDUMP) -h \
+	                               $(BUILD_DIR_BOARD)/$*.elf | grep -B1 LOAD | \
 	                               grep -Ev 'LOAD|\-\-' | awk '{print "0x" $$5}' | \
 	                               sort -g | head -1))
 	$(PYTHON) $(BSL) $(BSL_FLAGS) $(BSL_ADDRESS_ARG) $<
diff --git a/arch/platform/cooja/Makefile.cooja b/arch/platform/cooja/Makefile.cooja
index d06aa08d5..6a6a9d49e 100644
--- a/arch/platform/cooja/Makefile.cooja
+++ b/arch/platform/cooja/Makefile.cooja
@@ -34,10 +34,10 @@ endif
 
 endif ## QUICKSTART
 
-#MAIN_SRC = $(OBJECTDIR)/$(LIBNAME).c
-MAIN_OBJ = $(OBJECTDIR)/$(LIBNAME).o
-ARCHIVE = $(OBJECTDIR)/$(LIBNAME).a
-JNILIB = $(OBJECTDIR)/$(LIBNAME).$(TARGET)
+#MAIN_SRC = $(BUILD_DIR_BOARD)/$(LIBNAME).c
+MAIN_OBJ = $(BUILD_DIR_BOARD)/$(LIBNAME).o
+ARCHIVE = $(BUILD_DIR_BOARD)/$(LIBNAME).a
+JNILIB = $(BUILD_DIR_BOARD)/$(LIBNAME).$(TARGET)
 CONTIKI_APP_OBJ = $(CONTIKI_APP).o
 
 ### COOJA platform sources
diff --git a/arch/platform/cooja/Makefile.customrules-cooja b/arch/platform/cooja/Makefile.customrules-cooja
index 42d6e125e..60d6240f1 100644
--- a/arch/platform/cooja/Makefile.customrules-cooja
+++ b/arch/platform/cooja/Makefile.customrules-cooja
@@ -10,11 +10,11 @@ CUSTOM_RULE_LINK=1
 
 REDEF_PRINTF=1 # Redefine functions to enable printf()s inside Cooja
 
-# NB: Assumes ARCHIVE was not overridden and is in $(OBJECTDIR)
+# NB: Assumes ARCHIVE was not overridden and is in $(BUILD_DIR_BOARD)
 $(ARCHIVE): $(CONTIKI_OBJECTFILES) | $(OBJECTDIR)
 	$(AR_COMMAND_1) $^ $(AR_COMMAND_2)
 
-# NB: Assumes JNILIB was not overridden and is in $(OBJECTDIR)
+# NB: Assumes JNILIB was not overridden and is in $(BUILD_DIR_BOARD)
 $(JNILIB): $(CONTIKI_APP_OBJ) $(MAIN_OBJ) $(PROJECT_OBJECTFILES) $(ARCHIVE) | $(OBJECTDIR)
 
 ifdef REDEF_PRINTF
diff --git a/arch/platform/jn516x/Makefile.jn516x b/arch/platform/jn516x/Makefile.jn516x
index 9ad9488d5..051c336fb 100644
--- a/arch/platform/jn516x/Makefile.jn516x
+++ b/arch/platform/jn516x/Makefile.jn516x
@@ -229,30 +229,34 @@ ALLLIBS = $(addprefix -l,$(LDLIBS)) $(addprefix -l,$(LDSTACKLIBS)) $(addprefix -
 ABS_APPLIBS = $(addsuffix _$(JENNIC_CHIP_FAMILY).a,$(addprefix $(COMPONENTS_BASE_DIR)/Library/lib,$(APPLIBS)))
 
 ifneq ($(wildcard $(SDK_BASE_DIR)/Components/Library/*),)
-# The SDK is fully installed, proceed to linking and objcopy to ready-to-upload .jn516x.bin file
-%.$(TARGET): %.o $(PROJECT_OBJECTFILES) $(PROJECT_LIBRARIES) $(CONTIKI_NG_TARGET_LIB) $(ABS_APPLIBS)
-	echo  ${filter %.a,$^}
+# The SDK is fully installed, proceed to linking
+$(BUILD_DIR_BOARD)/%.$(TARGET): %.o $(PROJECT_OBJECTFILES) $(PROJECT_LIBRARIES) $(CONTIKI_NG_TARGET_LIB) $(ABS_APPLIBS)
+	@echo  ${filter %.a,$^}
 	$(Q)$(CC) -Wl,--gc-sections $(LDFLAGS) -T$(LINKCMD) -o $@ -Wl,--start-group \
 	  $(patsubst /cygdrive/c/%,c:/%,${filter-out %.a,$^}) \
 	  $(patsubst /cygdrive/c/%,c:/%,${filter %.a,$^}) \
 	  $(ALLLIBS) -Wl,--end-group -Wl,-Map,$(CONTIKI_NG_PROJECT_MAP)
-	$(OBJCOPY) -S -O binary $@ $@.bin
 else
 # The SDK does not include libraries, only build objects and libraries, skip linking
-%.$(TARGET): %.o $(PROJECT_OBJECTFILES) $(PROJECT_LIBRARIES) $(CONTIKI_NG_TARGET_LIB)
-	echo Creating empty $@
+$(BUILD_DIR_BOARD)/%.$(TARGET): %.o $(PROJECT_OBJECTFILES) $(PROJECT_LIBRARIES) $(CONTIKI_NG_TARGET_LIB)
+	@echo Creating empty $@
 	touch $@
 endif
 
-%.$(TARGET).bin: %.$(TARGET)
+$(BUILD_DIR_BOARD)/%.$(TARGET).bin: $(BUILD_DIR_BOARD)/%.$(TARGET)
+	$(TRACE_OBJCOPY)
 	$(Q)$(OBJCOPY) -S -O binary $< $@
 
+%.$(TARGET).bin: $(BUILD_DIR_BOARD)/%.$(TARGET).bin
+	$(TRACE_CP)
+	$(Q)$(CP) $< $@
+
 ### Upload target to one jn516x mote specified by MOTE=portNumber
 ifeq ($(HOST_OS),Windows)
-%.upload: %.$(TARGET).bin
+%.upload: $(BUILD_DIR_BOARD)/%.$(TARGET).bin
 	${FLASH_PROGRAMMER} -a -c $(DEV_PORT) -B 1000000 -s -w -f $<
 else
-%.upload: %.$(TARGET).bin
+%.upload: $(BUILD_DIR_BOARD)/%.$(TARGET).bin
 	${FLASH_PROGRAMMER} -V 10 -v -s $(DEV_PORT) -I 38400 -P 1000000 -f $<
 endif
 
@@ -276,7 +280,7 @@ motelistinfo:
 	$(Q)$(MOTELIST) ${FLASH_PROGRAMMER} \?
 
 ### Upload target to all connected jn516x motes
-%.uploadall: %.$(TARGET).bin
+%.uploadall: $(BUILD_DIR_BOARD)/%.$(TARGET).bin
 	$(Q)$(MOTELIST) ${FLASH_PROGRAMMER} $<
 
 ### Flash the given file to all connected jn516x motes
diff --git a/arch/platform/openmote-cc2538/Makefile.openmote-cc2538 b/arch/platform/openmote-cc2538/Makefile.openmote-cc2538
index d3863fdbc..8b25b0bfe 100644
--- a/arch/platform/openmote-cc2538/Makefile.openmote-cc2538
+++ b/arch/platform/openmote-cc2538/Makefile.openmote-cc2538
@@ -35,11 +35,12 @@ endif
 
 BSL = $(CONTIKI)/tools/cc2538-bsl/cc2538-bsl.py
 
-%.upload: %.bin %.elf
+%.upload: $(OUT_BIN) $(OUT_ELF)
 ifeq ($(wildcard $(BSL)), )
 	@echo "ERROR: Could not find the cc2538-bsl script. Did you run 'git submodule update --init' ?"
 else
-	$(eval BSL_ADDRESS_ARG := -a $(shell $(OBJDUMP) -h $*.elf | grep -B1 LOAD | \
+	$(eval BSL_ADDRESS_ARG := -a $(shell $(OBJDUMP) -h \
+	                               $(BUILD_DIR_BOARD)/$*.elf | grep -B1 LOAD | \
 	                               grep -Ev 'LOAD|\-\-' | awk '{print "0x" $$5}' | \
 	                               sort -g | head -1))
 	$(PYTHON) $(BSL) $(BSL_FLAGS) $(BSL_ADDRESS_ARG) $<
diff --git a/arch/platform/zoul/Makefile.zoul b/arch/platform/zoul/Makefile.zoul
index 938abe035..e43f84744 100644
--- a/arch/platform/zoul/Makefile.zoul
+++ b/arch/platform/zoul/Makefile.zoul
@@ -69,9 +69,9 @@ endif
 ### $$$$ Double escapes $s that need to be passed to the shell - once for when
 ### make parses UPLOAD_RULE, and once for when the expanded rule is parsed by make.
 define UPLOAD_RULE
-%.$(MOTE): %.bin %.elf
+%.$(MOTE): $(OUT_BIN) $(OUT_ELF)
 	@echo "Flashing $(MOTE)"
-	@BSL_ADDRESS=`$(OBJDUMP) -h $$*.elf | grep -B1 LOAD | \
+	@BSL_ADDRESS=`$(OBJDUMP) -h $(BUILD_DIR_BOARD)/$$*.elf | grep -B1 LOAD | \
 	             grep -Ev 'LOAD|\-\-' | awk '{print "0x" $$$$5}' | \
 	             sort -g | head -1`; \
 	$(PYTHON) $(BSL) $(BSL_FLAGS) -b $(BSL_SPEED) -a $$$${BSL_ADDRESS} -p $(MOTE) $$<
diff --git a/tools/cooja b/tools/cooja
index a5904b983..63538bbb8 160000
--- a/tools/cooja
+++ b/tools/cooja
@@ -1 +1 @@
-Subproject commit a5904b98366478bb9e7f7fe9f0bb78fc064914c5
+Subproject commit 63538bbb882ba06a7b8cf97c11ce2fe4d22e4f88