diff --git a/runtime/opae/Makefile b/runtime/opae/Makefile
index 153e33b3..168d5a11 100644
--- a/runtime/opae/Makefile
+++ b/runtime/opae/Makefile
@@ -1,13 +1,12 @@
 XLEN ?= 32
 TARGET ?= opaesim
 DESTDIR ?= $(CURDIR)
-OPAESIM_DIR = ../../sim/opaesim
-RTL_DIR=../../hw/rtl
-SYN_DIR=../../hw/syn/altera/opae
-SCRIPT_DIR=../../hw/scripts
+SIM_DIR = $(abspath ../../sim)
+HW_DIR = $(abspath ../../hw)
+SYN_DIR = $(HW_DIR)/syn/altera/opae
 
 CXXFLAGS += -std=c++11 -Wall -Wextra -pedantic -Wfatal-errors
-CXXFLAGS += -I$(DESTDIR) -I../include -I../common/ -I../../hw
+CXXFLAGS += -I../include -I../common -I$(HW_DIR) -I$(DESTDIR)
 CXXFLAGS += -DXLEN_$(XLEN)
 
 # Position independent code
@@ -26,7 +25,7 @@ SRCS = vortex.cpp driver.cpp ../common/utils.cpp
 # set up target types
 ifeq ($(TARGET), opaesim)
 	OPAESIM = $(DESTDIR)/libopae-c-sim.so
-	CXXFLAGS += -DOPAESIM -I$(OPAESIM_DIR)	
+	CXXFLAGS += -DOPAESIM -I$(SIM_DIR)/opaesim
 	LDFLAGS += -L$(DESTDIR) -lopae-c-sim
 else
 	CXXFLAGS += -I$(SYN_DIR)
@@ -60,11 +59,11 @@ PROJECT = libvortex.so
 all: $(DESTDIR)/$(PROJECT)
 
 $(DESTDIR)/libopae-c-sim.so:
-	DESTDIR=$(DESTDIR) $(MAKE) -C $(OPAESIM_DIR) $(DESTDIR)/libopae-c-sim.so
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIM_DIR)/opaesim $(DESTDIR)/libopae-c-sim.so
 
 $(DESTDIR)/$(PROJECT): $(SRCS) $(OPAESIM)
 	$(CXX) $(CXXFLAGS) $(SRCS) $(LDFLAGS) -o $@
 
 clean:
-	DESTDIR=$(DESTDIR) $(MAKE) -C $(OPAESIM_DIR) clean
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIM_DIR)/opaesim clean
 	rm -rf $(DESTDIR)/$(PROJECT)
diff --git a/runtime/rtlsim/Makefile b/runtime/rtlsim/Makefile
index 4b400f84..5f85bdc3 100644
--- a/runtime/rtlsim/Makefile
+++ b/runtime/rtlsim/Makefile
@@ -1,9 +1,10 @@
 XLEN ?= 32
 DESTDIR ?= $(CURDIR)
-RTLSIM_DIR = ../../sim/rtlsim
+SIM_DIR = $(abspath ../../sim)
+HW_DIR = $(abspath ../../hw)
 
 CXXFLAGS += -std=c++11 -Wall -Wextra -pedantic -Wfatal-errors
-CXXFLAGS += -I../include -I../common -I../../hw -I$(RTLSIM_DIR) -I$(RTLSIM_DIR)/../common
+CXXFLAGS += -I../include -I../common -I$(HW_DIR) -I$(SIM_DIR)/rtlsim -I$(SIM_DIR)/common
 CXXFLAGS += -DXLEN_$(XLEN)
 
 # Position independent code
@@ -37,9 +38,9 @@ PROJECT = libvortex.so
 all: $(DESTDIR)/$(PROJECT)
 	
 $(DESTDIR)/$(PROJECT): $(SRCS)
-	DESTDIR=$(DESTDIR) $(MAKE) -C $(RTLSIM_DIR) $(DESTDIR)/librtlsim.so
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIM_DIR)/rtlsim $(DESTDIR)/librtlsim.so
 	$(CXX) $(CXXFLAGS) $(SRCS) $(LDFLAGS) -o $@
 
 clean:
-	DESTDIR=$(DESTDIR) $(MAKE) -C $(RTLSIM_DIR) clean
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIM_DIR)/rtlsim clean
 	rm -rf $(DESTDIR)/$(PROJECT) *.o
\ No newline at end of file
diff --git a/runtime/simx/Makefile b/runtime/simx/Makefile
index 9397ec24..7cfd6c38 100644
--- a/runtime/simx/Makefile
+++ b/runtime/simx/Makefile
@@ -1,10 +1,11 @@
 XLEN ?= 32
 DESTDIR ?= $(CURDIR)
-SIMX_DIR = ../../sim/simx
+SIM_DIR = $(abspath ../../sim)
+HW_DIR = $(abspath ../../hw)
 
 CXXFLAGS += -std=c++11 -Wall -Wextra -Wfatal-errors
 CXXFLAGS += -fPIC -Wno-maybe-uninitialized
-CXXFLAGS += -I../include -I../common -I../../hw -I$(SIMX_DIR) -I$(SIMX_DIR)/../common
+CXXFLAGS += -I../include -I../common -I$(HW_DIR) -I$(SIM_DIR)/simx -I$(SIM_DIR)/common
 CXXFLAGS += $(CONFIGS)
 CXXFLAGS += -DDUMP_PERF_STATS
 CXXFLAGS += -DXLEN_$(XLEN)
@@ -26,9 +27,9 @@ PROJECT = libvortex.so
 all: $(DESTDIR)/$(PROJECT)
 
 $(DESTDIR)/$(PROJECT): $(SRCS)
-	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIMX_DIR) $(DESTDIR)/libsimx.so
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIM_DIR)/simx $(DESTDIR)/libsimx.so
 	$(CXX) $(CXXFLAGS) $^ $(LDFLAGS) -o $@
 
 clean:
-	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIMX_DIR) clean
+	DESTDIR=$(DESTDIR) $(MAKE) -C $(SIM_DIR)/simx clean
 	rm -rf $(DESTDIR)/$(PROJECT) *.o
\ No newline at end of file
diff --git a/runtime/stub/Makefile b/runtime/stub/Makefile
index 28441a3d..9c1c40bd 100644
--- a/runtime/stub/Makefile
+++ b/runtime/stub/Makefile
@@ -1,6 +1,11 @@
+XLEN ?= 32
+DESTDIR ?= $(CURDIR)
+SIM_DIR = $(abspath ../../sim)
+HW_DIR = $(abspath ../../hw)
+
 CXXFLAGS += -std=c++11 -O2 -Wall -Wextra -pedantic -Wfatal-errors
 
-CXXFLAGS += -I../include -I../../runtime -I../../hw -I../../sim/common
+CXXFLAGS += -I../include -I../common -I$(HW_DIR) -I$(SIM_DIR)/common
 
 CXXFLAGS += -fPIC
 
diff --git a/sim/opaesim/Makefile b/sim/opaesim/Makefile
index 93f2da33..97c8aaf7 100644
--- a/sim/opaesim/Makefile
+++ b/sim/opaesim/Makefile
@@ -1,20 +1,22 @@
 XLEN ?= 32
 DESTDIR ?= $(CURDIR)
-RTL_DIR = ../../hw/rtl
-DPI_DIR = ../../hw/dpi
+HW_DIR = $(abspath ../../hw)
+COMMON_DIR = $(abspath ../common)
+THIRD_PARTY_DIR = $(abspath ../../third_party)
+RTL_DIR = $(HW_DIR)/rtl
+DPI_DIR = $(HW_DIR)/dpi
 AFU_DIR = $(RTL_DIR)/afu/opae
-SCRIPT_DIR = ../../hw/scripts
-THIRD_PARTY_DIR = ../../third_party
+SCRIPT_DIR = $(HW_DIR)/scripts
 
 CXXFLAGS += -std=c++11 -Wall -Wextra -Wfatal-errors -Wno-array-bounds
 CXXFLAGS += -fPIC -Wno-maybe-uninitialized
-CXXFLAGS += -I.. -I../../../hw -I../../common -I$(abspath $(DESTDIR))
-CXXFLAGS += -I../$(THIRD_PARTY_DIR)/softfloat/source/include
-CXXFLAGS += -I../$(THIRD_PARTY_DIR)
+CXXFLAGS += -I$(CURDIR) -I$(HW_DIR) -I$(COMMON_DIR) -I$(DESTDIR)
+CXXFLAGS += -I/$(THIRD_PARTY_DIR)/softfloat/source/include
+CXXFLAGS += -I/$(THIRD_PARTY_DIR)
 CXXFLAGS += -DXLEN_$(XLEN)
 
-LDFLAGS += -shared ../$(THIRD_PARTY_DIR)/softfloat/build/Linux-x86_64-GCC/softfloat.a
-LDFLAGS += -L../$(THIRD_PARTY_DIR)/ramulator -lramulator -pthread
+LDFLAGS += -shared $(THIRD_PARTY_DIR)/softfloat/build/Linux-x86_64-GCC/softfloat.a
+LDFLAGS += -L$(THIRD_PARTY_DIR)/ramulator -lramulator -pthread
 
 # control RTL debug tracing states
 DBG_TRACE_FLAGS += -DDBG_TRACE_CORE_PIPELINE  
@@ -53,9 +55,9 @@ endif
 
 DBG_FLAGS += -DDEBUG_LEVEL=$(DEBUG) -DVCD_OUTPUT $(DBG_TRACE_FLAGS)
 
-SRCS = ../common/util.cpp ../common/mem.cpp ../common/rvfloats.cpp
+SRCS = $(COMMON_DIR)/util.cpp $(COMMON_DIR)/mem.cpp $(COMMON_DIR)/rvfloats.cpp
 SRCS += $(DPI_DIR)/util_dpi.cpp $(DPI_DIR)/float_dpi.cpp
-SRCS += fpga.cpp opae_sim.cpp
+SRCS += $(CURDIR)/fpga.cpp $(CURDIR)/opae_sim.cpp
 
 RTL_PKGS = $(AFU_DIR)/local_mem_cfg_pkg.sv $(AFU_DIR)/ccip/ccip_if_pkg.sv
 RTL_PKGS += $(RTL_DIR)/VX_gpu_pkg.sv $(RTL_DIR)/fpu/VX_fpu_pkg.sv
@@ -128,7 +130,7 @@ $(DESTDIR)/vortex_afu.h : $(AFU_DIR)/vortex_afu.vh
 	$(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 $@
+	verilator --build --exe -O3 $(VL_FLAGS) --cc $(TOP) --top-module $(TOP) $(SRCS) -CFLAGS '$(CXXFLAGS)' -LDFLAGS '$(LDFLAGS)' --Mdir $(DESTDIR)/obj_dir -o $@
 
 clean:
-	rm -rf obj_dir $(DESTDIR)/vortex.xml $(DESTDIR)/scope.json $(DESTDIR)/vortex_afu.h $(DESTDIR)/$(PROJECT)
+	rm -rf $(DESTDIR)/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 228cdd8b..3734a03b 100644
--- a/sim/rtlsim/Makefile
+++ b/sim/rtlsim/Makefile
@@ -1,18 +1,20 @@
 XLEN ?= 32
 DESTDIR ?= $(CURDIR)
-RTL_DIR = ../../hw/rtl
-DPI_DIR = ../../hw/dpi
-THIRD_PARTY_DIR = ../../third_party
+HW_DIR = $(abspath ../../hw)
+COMMON_DIR = $(abspath ../common)
+THIRD_PARTY_DIR = $(abspath ../../third_party)
+RTL_DIR = $(HW_DIR)/rtl
+DPI_DIR = $(HW_DIR)/dpi
 
 CXXFLAGS += -std=c++11 -Wall -Wextra -Wfatal-errors -Wno-array-bounds
 CXXFLAGS += -fPIC -Wno-maybe-uninitialized
-CXXFLAGS += -I../../../hw -I../../common
-CXXFLAGS += -I../$(THIRD_PARTY_DIR)/softfloat/source/include
-CXXFLAGS += -I../$(THIRD_PARTY_DIR)
+CXXFLAGS += -I$(HW_DIR) -I$(COMMON_DIR)
+CXXFLAGS += -I$(THIRD_PARTY_DIR)/softfloat/source/include
+CXXFLAGS += -I$(THIRD_PARTY_DIR)
 CXXFLAGS += -DXLEN_$(XLEN)
 
-LDFLAGS += ../$(THIRD_PARTY_DIR)/softfloat/build/Linux-x86_64-GCC/softfloat.a
-LDFLAGS += -L../$(THIRD_PARTY_DIR)/ramulator -lramulator
+LDFLAGS += $(THIRD_PARTY_DIR)/softfloat/build/Linux-x86_64-GCC/softfloat.a
+LDFLAGS += -L$(THIRD_PARTY_DIR)/ramulator -lramulator
 
 # control RTL debug tracing states
 DBG_TRACE_FLAGS += -DDBG_TRACE_CORE_PIPELINE  
@@ -38,9 +40,9 @@ ifneq (,$(findstring FPU_FPNEW,$(CONFIGS)))
 endif
 RTL_INCLUDE = -I$(RTL_DIR) -I$(DPI_DIR) -I$(RTL_DIR)/libs -I$(RTL_DIR)/interfaces -I$(RTL_DIR)/core -I$(RTL_DIR)/mem -I$(RTL_DIR)/cache $(FPU_INCLUDE)
 
-SRCS = ../common/util.cpp ../common/mem.cpp ../common/rvfloats.cpp
+SRCS = $(COMMON_DIR)/util.cpp $(COMMON_DIR)/mem.cpp $(COMMON_DIR)/rvfloats.cpp
 SRCS += $(DPI_DIR)/util_dpi.cpp $(DPI_DIR)/float_dpi.cpp
-SRCS += processor.cpp
+SRCS += $(CURDIR)/processor.cpp
 
 ifdef AXI_BUS
 	TOP = Vortex_axi
@@ -87,11 +89,11 @@ PROJECT = rtlsim
 
 all: $(DESTDIR)/$(PROJECT)
 
-$(DESTDIR)/$(PROJECT): $(SRCS) main.cpp
-	verilator --build $(VL_FLAGS) $^ -CFLAGS '$(CXXFLAGS) -DSTARTUP_ADDR=0x80000000' -LDFLAGS '$(LDFLAGS)' -o $@
+$(DESTDIR)/$(PROJECT): $(SRCS) $(CURDIR)/main.cpp
+	verilator --build $(VL_FLAGS) $^ -CFLAGS '$(CXXFLAGS) -DSTARTUP_ADDR=0x80000000' -LDFLAGS '$(LDFLAGS)' --Mdir $(DESTDIR)/obj_dir -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)' --Mdir $(DESTDIR)/obj_dir -o $@
 
 clean:
-	rm -rf obj_dir $(DESTDIR)/$(PROJECT) $(DESTDIR)/lib$(PROJECT).so
+	rm -rf $(DESTDIR)/obj_dir $(DESTDIR)/$(PROJECT) $(DESTDIR)/lib$(PROJECT).so
diff --git a/sim/simx/Makefile b/sim/simx/Makefile
index 3cce8de0..36f0b63e 100644
--- a/sim/simx/Makefile
+++ b/sim/simx/Makefile
@@ -1,11 +1,12 @@
 XLEN ?= 32
 DESTDIR ?= $(CURDIR)
-RTL_DIR = ../hw/rtl
-THIRD_PARTY_DIR = ../../third_party
+HW_DIR = $(abspath ../../hw)
+COMMON_DIR = $(abspath ../common)
+THIRD_PARTY_DIR = $(abspath ../../third_party)
 
 CXXFLAGS += -std=c++17 -Wall -Wextra -Wfatal-errors
 CXXFLAGS += -fPIC -Wno-maybe-uninitialized
-CXXFLAGS += -I. -I../common -I../../hw
+CXXFLAGS += -I$(CURDIR) -I$(COMMON_DIR) -I$(HW_DIR)
 CXXFLAGS += -I$(THIRD_PARTY_DIR)/softfloat/source/include
 CXXFLAGS += -I$(THIRD_PARTY_DIR)
 CXXFLAGS += -DXLEN_$(XLEN)
@@ -14,7 +15,7 @@ CXXFLAGS += $(CONFIGS)
 LDFLAGS += $(THIRD_PARTY_DIR)/softfloat/build/Linux-x86_64-GCC/softfloat.a
 LDFLAGS += -L$(THIRD_PARTY_DIR)/ramulator -lramulator
 
-SRCS = ../common/util.cpp ../common/mem.cpp ../common/rvfloats.cpp
+SRCS = $(COMMON_DIR)/util.cpp $(COMMON_DIR)/mem.cpp $(COMMON_DIR)/rvfloats.cpp
 SRCS += processor.cpp cluster.cpp socket.cpp core.cpp warp.cpp decode.cpp execute.cpp exe_unit.cpp cache_sim.cpp mem_sim.cpp shared_mem.cpp dcrs.cpp
 
 # Debugigng