diff --git a/ci/blackbox.sh b/ci/blackbox.sh
index 5e06ae65..d5deacec 100755
--- a/ci/blackbox.sh
+++ b/ci/blackbox.sh
@@ -16,7 +16,17 @@
 show_usage()
 {
     echo "Vortex BlackBox Test Driver v1.0"
-    echo "Usage: $0 [[--clusters=#n] [--cores=#n] [--warps=#n] [--threads=#n] [--l2cache] [--l3cache] [[--driver=#name] [--app=#app] [--args=#args] [--debug=#level] [--scope] [--perf=#class] [--rebuild=0|1] [--log=logfile] [--help]]"
+    echo "Usage: $0 [[--clusters=#n] [--cores=#n] [--warps=#n] [--threads=#n] [--l2cache] [--l3cache] [[--driver=#name] [--app=#app] [--args=#args] [--debug=#level] [--scope] [--perf=#class] [--rebuild=#n] [--log=logfile] [--help]]"
+}
+
+show_help()
+{
+    show_usage
+    echo "  where"
+    echo "--driver: simx, rtlsim, oape, xrt"
+    echo "--app: any subfolder test under regression or opencl"
+    echo "--class: 0=disable, 1=pipeline, 2=memsys"
+    echo "--rebuild: 0=disable, 1=force, 2=auto, 3=temp"
 }
 
 SCRIPT_DIR=$(dirname "$0")
@@ -36,6 +46,7 @@ SCOPE=0
 HAS_ARGS=0
 PERF_CLASS=0
 REBUILD=2
+TEMPBUILD=0
 LOGFILE=run.log
 
 for i in "$@"
@@ -102,7 +113,7 @@ case $i in
         shift
         ;;
     --help)
-        show_usage
+        show_help
         exit 0
         ;;
     *)
@@ -112,6 +123,12 @@ case $i in
 esac
 done
 
+if [ $REBUILD -eq 3 ];
+then
+    REBUILD=1
+    TEMPBUILD=1
+fi
+
 case $DRIVER in
     simx)
         DRIVER_PATH=$VORTEX_HOME/runtime/simx
@@ -174,53 +191,119 @@ make -C $VORTEX_HOME/runtime/stub > /dev/null
 
 if [ $DEBUG -ne 0 ]
 then    
-    # driver initialization
-    if [ $SCOPE -eq 1 ]
-    then
-        echo "running: DEBUG=$DEBUG_LEVEL SCOPE=1 CONFIGS="$CONFIGS" make -C $DRIVER_PATH"
-        DEBUG=$DEBUG_LEVEL SCOPE=1 CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
-    else
-        echo "running: DEBUG=$DEBUG_LEVEL CONFIGS="$CONFIGS" make -C $DRIVER_PATH"
-        DEBUG=$DEBUG_LEVEL CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
-    fi
-    
     # running application
-    if [ $HAS_ARGS -eq 1 ]
+    if [ $TEMPBUILD -eq 1 ]
     then
-        echo "running: OPTS=$ARGS make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1"
-        OPTS=$ARGS make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1
-        status=$?
+        # setup temp directory
+        TEMPDIR=$(mktemp -d)
+        mkdir -p "$TEMPDIR/$DRIVER"
+
+        # driver initialization
+        if [ $SCOPE -eq 1 ]
+        then
+            echo "running: DESTDIR=$TEMPDIR/$DRIVER DEBUG=$DEBUG_LEVEL SCOPE=1 CONFIGS=$CONFIGS make -C $DRIVER_PATH"
+            DESTDIR="$TEMPDIR/$DRIVER" DEBUG=$DEBUG_LEVEL SCOPE=1 CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        else
+            echo "running: DESTDIR=$TEMPDIR/$DRIVER DEBUG=$DEBUG_LEVEL CONFIGS=$CONFIGS make -C $DRIVER_PATH"
+            DESTDIR="$TEMPDIR/$DRIVER" DEBUG=$DEBUG_LEVEL CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        fi
+
+        # running application
+        if [ $HAS_ARGS -eq 1 ]
+        then
+            echo "running: VORTEX_RT_PATH=$TEMPDIR OPTS=$ARGS make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1"
+            VORTEX_RT_PATH=$TEMPDIR OPTS=$ARGS make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1
+            status=$?
+        else
+            echo "running: VORTEX_RT_PATH=$TEMPDIR make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1"
+            VORTEX_RT_PATH=$TEMPDIR make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1
+            status=$?
+        fi
+
+        # cleanup temp directory
+        trap "rm -rf $TEMPDIR" EXIT
     else
-        echo "running: make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1"
-        make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1
-        status=$?
+        # driver initialization
+        if [ $SCOPE -eq 1 ]
+        then
+            echo "running: DEBUG=$DEBUG_LEVEL SCOPE=1 CONFIGS=$CONFIGS make -C $DRIVER_PATH"
+            DEBUG=$DEBUG_LEVEL SCOPE=1 CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        else
+            echo "running: DEBUG=$DEBUG_LEVEL CONFIGS=$CONFIGS make -C $DRIVER_PATH"
+            DEBUG=$DEBUG_LEVEL CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        fi
+
+        # running application
+        if [ $HAS_ARGS -eq 1 ]
+        then
+            echo "running: OPTS=$ARGS make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1"
+            OPTS=$ARGS make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1
+            status=$?
+        else
+            echo "running: make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1"
+            make -C $APP_PATH run-$DRIVER > $LOGFILE 2>&1
+            status=$?
+        fi
     fi
     
     if [ -f "$APP_PATH/trace.vcd" ]
     then 
         mv -f $APP_PATH/trace.vcd .
     fi
-else
-    # driver initialization
-    if [ $SCOPE -eq 1 ]
+else    
+    if [ $TEMPBUILD -eq 1 ]
     then
-        echo "running: SCOPE=1 CONFIGS="$CONFIGS" make -C $DRIVER_PATH"
-        SCOPE=1 CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        # setup temp directory
+        TEMPDIR=$(mktemp -d)
+        mkdir -p "$TEMPDIR/$DRIVER"
+        
+        # driver initialization
+        if [ $SCOPE -eq 1 ]
+        then
+            echo "running: DESTDIR=$TEMPDIR/$DRIVER SCOPE=1 CONFIGS=$CONFIGS make -C $DRIVER_PATH"
+            DESTDIR="$TEMPDIR/$DRIVER" SCOPE=1 CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        else
+            echo "running: DESTDIR=$TEMPDIR/$DRIVER CONFIGS=$CONFIGS make -C $DRIVER_PATH"
+            DESTDIR="$TEMPDIR/$DRIVER" CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        fi
+        
+        # running application
+        if [ $HAS_ARGS -eq 1 ]
+        then
+            echo "running: VORTEX_RT_PATH=$TEMPDIR OPTS=$ARGS make -C $APP_PATH run-$DRIVER"
+            VORTEX_RT_PATH=$TEMPDIR OPTS=$ARGS make -C $APP_PATH run-$DRIVER
+            status=$?
+        else
+            echo "running: VORTEX_RT_PATH=$TEMPDIR make -C $APP_PATH run-$DRIVER"
+            VORTEX_RT_PATH=$TEMPDIR make -C $APP_PATH run-$DRIVER
+            status=$?
+        fi
+
+        # cleanup temp directory
+        trap "rm -rf $TEMPDIR" EXIT
     else
-        echo "running: CONFIGS="$CONFIGS" make -C $DRIVER_PATH"
-        CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
-    fi
-    
-    # running application
-    if [ $HAS_ARGS -eq 1 ]
-    then
-        echo "running: OPTS=$ARGS make -C $APP_PATH run-$DRIVER"
-        OPTS=$ARGS make -C $APP_PATH run-$DRIVER
-        status=$?
-    else
-        echo "running: make -C $APP_PATH run-$DRIVER"
-        make -C $APP_PATH run-$DRIVER
-        status=$?
+        
+        # driver initialization
+        if [ $SCOPE -eq 1 ]
+        then
+            echo "running: SCOPE=1 CONFIGS=$CONFIGS make -C $DRIVER_PATH"
+            SCOPE=1 CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        else
+            echo "running: CONFIGS=$CONFIGS make -C $DRIVER_PATH"
+            CONFIGS="$CONFIGS" make -C $DRIVER_PATH > /dev/null
+        fi
+
+        # running application
+        if [ $HAS_ARGS -eq 1 ]
+        then
+            echo "running: OPTS=$ARGS make -C $APP_PATH run-$DRIVER"
+            OPTS=$ARGS make -C $APP_PATH run-$DRIVER
+            status=$?
+        else
+            echo "running: make -C $APP_PATH run-$DRIVER"
+            make -C $APP_PATH run-$DRIVER
+            status=$?
+        fi
     fi
 fi
 
diff --git a/runtime/opae/Makefile b/runtime/opae/Makefile
index 82d0b69c..153e33b3 100644
--- a/runtime/opae/Makefile
+++ b/runtime/opae/Makefile
@@ -1,25 +1,15 @@
 XLEN ?= 32
-
 TARGET ?= opaesim
-
+DESTDIR ?= $(CURDIR)
 OPAESIM_DIR = ../../sim/opaesim
-
 RTL_DIR=../../hw/rtl
-
 SYN_DIR=../../hw/syn/altera/opae
-
 SCRIPT_DIR=../../hw/scripts
 
 CXXFLAGS += -std=c++11 -Wall -Wextra -pedantic -Wfatal-errors
-CXXFLAGS += -I. -I../include -I../common/ -I../../hw
+CXXFLAGS += -I$(DESTDIR) -I../include -I../common/ -I../../hw
 CXXFLAGS += -DXLEN_$(XLEN)
 
-ifeq ($(TARGET), opaesim)
-	CXXFLAGS += -I$(OPAESIM_DIR)
-else
-	CXXFLAGS += -I$(SYN_DIR)
-endif
-
 # Position independent code
 CXXFLAGS += -fPIC
 
@@ -35,9 +25,11 @@ SRCS = vortex.cpp driver.cpp ../common/utils.cpp
 
 # set up target types
 ifeq ($(TARGET), opaesim)
-	CXXFLAGS += -DOPAESIM
-	OPAESIM = libopae-c-sim.so
+	OPAESIM = $(DESTDIR)/libopae-c-sim.so
+	CXXFLAGS += -DOPAESIM -I$(OPAESIM_DIR)	
+	LDFLAGS += -L$(DESTDIR) -lopae-c-sim
 else
+	CXXFLAGS += -I$(SYN_DIR)
 	ifeq ($(TARGET), asesim)
 		CXXFLAGS += -DASESIM
 	else
@@ -65,14 +57,14 @@ endif
 
 PROJECT = libvortex.so
 
-all: $(PROJECT)
+all: $(DESTDIR)/$(PROJECT)
 
-libopae-c-sim.so:
-	DESTDIR=../../runtime/opae $(MAKE) -C $(OPAESIM_DIR) ../../runtime/opae/libopae-c-sim.so
+$(DESTDIR)/libopae-c-sim.so:
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(OPAESIM_DIR) $(DESTDIR)/libopae-c-sim.so
 
-$(PROJECT): $(SRCS) $(OPAESIM)
-	$(CXX) $(CXXFLAGS) $(SRCS) $(LDFLAGS) -o $(PROJECT)
+$(DESTDIR)/$(PROJECT): $(SRCS) $(OPAESIM)
+	$(CXX) $(CXXFLAGS) $(SRCS) $(LDFLAGS) -o $@
 
 clean:
-	DESTDIR=../../runtime/opae $(MAKE) -C $(OPAESIM_DIR) clean
-	rm -rf $(PROJECT)
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(OPAESIM_DIR) clean
+	rm -rf $(DESTDIR)/$(PROJECT)
diff --git a/runtime/rtlsim/Makefile b/runtime/rtlsim/Makefile
index 57f58df4..4b400f84 100644
--- a/runtime/rtlsim/Makefile
+++ b/runtime/rtlsim/Makefile
@@ -1,5 +1,5 @@
 XLEN ?= 32
-
+DESTDIR ?= $(CURDIR)
 RTLSIM_DIR = ../../sim/rtlsim
 
 CXXFLAGS += -std=c++11 -Wall -Wextra -pedantic -Wfatal-errors
@@ -16,7 +16,7 @@ CXXFLAGS += $(CONFIGS)
 CXXFLAGS += -DDUMP_PERF_STATS
 
 LDFLAGS += -shared -pthread
-LDFLAGS += -L. -lrtlsim
+LDFLAGS += -L$(DESTDIR) -lrtlsim
 
 SRCS = vortex.cpp ../common/utils.cpp
 
@@ -34,12 +34,12 @@ endif
 
 PROJECT = libvortex.so
 
-all: $(PROJECT)
+all: $(DESTDIR)/$(PROJECT)
 	
-$(PROJECT): $(SRCS)
-	DESTDIR=../../runtime/rtlsim $(MAKE) -C $(RTLSIM_DIR) ../../runtime/rtlsim/librtlsim.so
-	$(CXX) $(CXXFLAGS) $(SRCS) $(LDFLAGS) -o $(PROJECT)
+$(DESTDIR)/$(PROJECT): $(SRCS)
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(RTLSIM_DIR) $(DESTDIR)/librtlsim.so
+	$(CXX) $(CXXFLAGS) $(SRCS) $(LDFLAGS) -o $@
 
 clean:
-	DESTDIR=../../runtime/rtlsim $(MAKE) -C $(RTLSIM_DIR) clean
-	rm -rf $(PROJECT) *.o
\ No newline at end of file
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(RTLSIM_DIR) clean
+	rm -rf $(DESTDIR)/$(PROJECT) *.o
\ No newline at end of file
diff --git a/runtime/simx/Makefile b/runtime/simx/Makefile
index c9f157fd..9397ec24 100644
--- a/runtime/simx/Makefile
+++ b/runtime/simx/Makefile
@@ -1,5 +1,5 @@
 XLEN ?= 32
-
+DESTDIR ?= $(CURDIR)
 SIMX_DIR = ../../sim/simx
 
 CXXFLAGS += -std=c++11 -Wall -Wextra -Wfatal-errors
@@ -10,7 +10,7 @@ CXXFLAGS += -DDUMP_PERF_STATS
 CXXFLAGS += -DXLEN_$(XLEN)
 
 LDFLAGS += -shared -pthread
-LDFLAGS += -L. -lsimx
+LDFLAGS += -L$(DESTDIR) -lsimx
 
 SRCS = vortex.cpp ../common/utils.cpp
 
@@ -23,12 +23,12 @@ endif
 
 PROJECT = libvortex.so
 
-all: $(PROJECT)
+all: $(DESTDIR)/$(PROJECT)
 
-$(PROJECT): $(SRCS)
-	DESTDIR=../../runtime/simx $(MAKE) -C $(SIMX_DIR) ../../runtime/simx/libsimx.so
+$(DESTDIR)/$(PROJECT): $(SRCS)
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIMX_DIR) $(DESTDIR)/libsimx.so
 	$(CXX) $(CXXFLAGS) $^ $(LDFLAGS) -o $@
 
 clean:
-	DESTDIR=../../runtime/simx $(MAKE) -C $(SIMX_DIR) clean
-	rm -rf libsimx.so $(PROJECT) *.o
\ No newline at end of file
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIMX_DIR) clean
+	rm -rf $(DESTDIR)/$(PROJECT) *.o
\ No newline at end of file
diff --git a/sim/opaesim/Makefile b/sim/opaesim/Makefile
index 3b906bc5..93f2da33 100644
--- a/sim/opaesim/Makefile
+++ b/sim/opaesim/Makefile
@@ -1,5 +1,5 @@
 XLEN ?= 32
-DESTDIR ?= .
+DESTDIR ?= $(CURDIR)
 RTL_DIR = ../../hw/rtl
 DPI_DIR = ../../hw/dpi
 AFU_DIR = $(RTL_DIR)/afu/opae
@@ -119,16 +119,16 @@ PROJECT = libopae-c-sim.so
 all: $(DESTDIR)/$(PROJECT)
 
 $(DESTDIR)/vortex.xml:
-	verilator --xml-only -O0 $(VL_FLAGS) $(TOP) --xml-output $(DESTDIR)/vortex.xml
+	verilator --xml-only -O0 $(VL_FLAGS) $(TOP) --xml-output $@
 
 $(DESTDIR)/scope.json: $(DESTDIR)/vortex.xml
-	$(SCRIPT_DIR)/scope.py $(DESTDIR)/vortex.xml -o $(DESTDIR)/scope.json
+	$(SCRIPT_DIR)/scope.py $^ -o $@
 
 $(DESTDIR)/vortex_afu.h : $(AFU_DIR)/vortex_afu.vh
-	$(SCRIPT_DIR)/gen_config.py -i $(AFU_DIR)/vortex_afu.vh -o $(DESTDIR)/vortex_afu.h
+	$(SCRIPT_DIR)/gen_config.py -i $^ -o $@
 
 $(DESTDIR)/$(PROJECT): $(SRCS) $(DESTDIR)/vortex_afu.h $(SCOPE_JSON)
-	verilator --build --exe -O3 $(VL_FLAGS) --cc $(TOP) --top-module $(TOP) $(SRCS) -CFLAGS '$(CXXFLAGS)' -LDFLAGS '$(LDFLAGS)' -o ../$(DESTDIR)/$(PROJECT)
+	verilator --build --exe -O3 $(VL_FLAGS) --cc $(TOP) --top-module $(TOP) $(SRCS) -CFLAGS '$(CXXFLAGS)' -LDFLAGS '$(LDFLAGS)' -o $@
 
 clean:
 	rm -rf obj_dir $(DESTDIR)/vortex.xml $(DESTDIR)/scope.json $(DESTDIR)/vortex_afu.h $(DESTDIR)/$(PROJECT)
diff --git a/sim/rtlsim/Makefile b/sim/rtlsim/Makefile
index 1d43ea4f..228cdd8b 100644
--- a/sim/rtlsim/Makefile
+++ b/sim/rtlsim/Makefile
@@ -1,5 +1,5 @@
 XLEN ?= 32
-DESTDIR ?= .
+DESTDIR ?= $(CURDIR)
 RTL_DIR = ../../hw/rtl
 DPI_DIR = ../../hw/dpi
 THIRD_PARTY_DIR = ../../third_party
@@ -88,10 +88,10 @@ PROJECT = rtlsim
 all: $(DESTDIR)/$(PROJECT)
 
 $(DESTDIR)/$(PROJECT): $(SRCS) main.cpp
-	verilator --build $(VL_FLAGS) $^ -CFLAGS '$(CXXFLAGS) -DSTARTUP_ADDR=0x80000000' -LDFLAGS '$(LDFLAGS)' -o ../$@
+	verilator --build $(VL_FLAGS) $^ -CFLAGS '$(CXXFLAGS) -DSTARTUP_ADDR=0x80000000' -LDFLAGS '$(LDFLAGS)' -o $@
 	
 $(DESTDIR)/lib$(PROJECT).so: $(SRCS)
-	verilator --build $(VL_FLAGS) $^ -CFLAGS '$(CXXFLAGS)' -LDFLAGS '-shared $(LDFLAGS)' -o ../$@
+	verilator --build $(VL_FLAGS) $^ -CFLAGS '$(CXXFLAGS)' -LDFLAGS '-shared $(LDFLAGS)' -o $@
 
 clean:
 	rm -rf obj_dir $(DESTDIR)/$(PROJECT) $(DESTDIR)/lib$(PROJECT).so
diff --git a/sim/simx/Makefile b/sim/simx/Makefile
index bb67dbb5..3cce8de0 100644
--- a/sim/simx/Makefile
+++ b/sim/simx/Makefile
@@ -1,5 +1,5 @@
 XLEN ?= 32
-DESTDIR ?= .
+DESTDIR ?= $(CURDIR)
 RTL_DIR = ../hw/rtl
 THIRD_PARTY_DIR = ../../third_party