diff --git a/LibOS/shim/test/Makefile b/LibOS/shim/test/Makefile
index 08b0e644..10740882 100644
--- a/LibOS/shim/test/Makefile
+++ b/LibOS/shim/test/Makefile
@@ -1,94 +1,14 @@
-subdirs = native
+# SUBDIRS = regression native inline benchmark
+SUBDIRS = native
 
 SYS ?= $(shell gcc -dumpmachine)
 export SYS
 
-PALDIR  = $(level)../../../Pal/src
-SHIMDIR = $(level)../src
-RUNTIME = $(level)../../../Runtime
-
-ifeq ($(SGX),1)
-PAL_LOADER = pal_loader SGX
-else
-PAL_LOADER = pal_loader
-endif
-
-CC = gcc
-CXX = g++
-CFLAGS 	= -Wall -std=gnu99
-CFLAGS-debug = -I$(SHIMDIR)/../include -I$(PALDIR)/../include/pal -I$(PALDIR)/../lib
-CXXFLAGS = -Wall -std=c++14
-CXXFLAGS-debug = -I$(SHIMDIR)/../include -I$(PALDIR)/../include/pal -I$(PALDIR)/../lib
-LDFLAGS	=
-LDFLAGS-debug = -L$(SHIMDIR) -L$(PALDIR) -Wl,-rpath-link=$(abspath $(RUNTIME))
-
-CFLAGS-libos = -I$(SHIMDIR)/../include -L$(SHIMDIR)/../../glibc-build/libos
-
 .PHONY: default
 default: all
 
-include $(level)../../../Makefile.configs
-include $(level)../../../Makefile.rules
-include $(PALDIR)/Makefile.Test
-
-.PHONY: all
-all: pal_loader $(target) $(if $(level),,build-subdirs) | $(call expand_target,$(exec_target))
-
-ifeq ($(DEBUG),1)
-CC += -g
-CXX += -g
-endif
-export DEBUG
-
-ifeq ($(WERROR),1)
-CFLAGS += -Werror
-endif
-
-ifeq ($(ABSPATH_IN_MANIFEST),yes)
-manifest_rules = \
-	-e 's:\$$(PAL):$(abspath $(RUNTIME))/$(PAL_LOADER):g' \
-	-e 's:\$$(PWD):$(PWD):g' \
-	-e 's:\$$(BIN):$(subst .manifest,,$(notdir $@)):g' \
-	-e 's:\$$(SHIMPATH):$(abspath $(RUNTIME))/libsysdb.so:g' \
-	-e 's:\$$(LIBCDIR):$(abspath $(RUNTIME)):g' \
-	$(extra_rules)
-else
-manifest_rules= \
-	-e 's:\$$(PAL):$(abspath $(RUNTIME))/$(PAL_LOADER):g' \
-	-e 's:\$$(PWD):$(PWD):g' \
-	-e 's:\$$(BIN):$(subst .manifest,,$(notdir $@)):g' \
-	-e 's:\$$(SHIMPATH):'$$RELDIR'$(RUNTIME)/libsysdb.so:g' \
-	-e 's:\$$(LIBCDIR):'$$RELDIR'$(RUNTIME):g' \
-	$(extra_rules)
-endif
-
-pal_loader:
-	ln -sf $(RUNTIME)/pal_loader
-
-relative-to = $(shell python -c "import os.path; print os.path.relpath(\"$(abspath $2)\",\"$(abspath $1)\")")
-
-%manifest: %manifest.template
-	@echo [ $@ ]
-	RELDIR=$(filter-out ./,$(call relative-to,$(dir $@),$(shell pwd))/) && \
-	sed $(manifest_rules) $< > $@
-	(grep -q '^#!' $@ && chmod +x $@) || true
-
-manifest: manifest.template
-	@echo [ $@ ]
-	sed $(manifest_rules) $< > $@
-
-ifeq ($(SGX), 1)
-include $(addsuffix .manifest.sgx.d,$(patsubst %.manifest,%,$(exec_target)))
-endif
-
-.PHONY: clean
-clean: $(clean-extra) $(if $(level),,clean-subdirs)
-	rm -rf pal_loader $(call expand_target,$(exec_target)) $(target) $(wildcard *.d)
-
-.PHONY: build-subdirs
-build-subdirs:
-	for f in $(subdirs); do (cd $$f; $(MAKE); cd ..); done
-
-.PHONY: clean-subdirs
-clean-subdirs:
-	for f in $(subdirs); do (cd $$f; $(MAKE) clean; cd ..); done
+.PHONY: all clean
+all clean:
+	for d in $(SUBDIRS); do \
+		$(MAKE) -C $$d $@; \
+	done
diff --git a/LibOS/shim/test/Makefile.Test b/LibOS/shim/test/Makefile.Test
index e07042a9..f15eb459 100644
--- a/LibOS/shim/test/Makefile.Test
+++ b/LibOS/shim/test/Makefile.Test
@@ -28,6 +28,8 @@ LDFLAGS-libos-debug = -L$(SHIMDIR) -L$(PALDIR)/host/$(PAL_HOST) -Wl,-rpath-link=
 .PHONY: default
 default: all
 
+include $(SHIM_TEST_DIR)/../../../Makefile.configs
+include $(SHIM_TEST_DIR)/../../../Makefile.rules
 include $(PALDIR)/Makefile.Test
 
 .PHONY: all
@@ -66,7 +68,7 @@ pal_loader:
 
 relative-to = $(shell python -c "import os.path; print os.path.relpath(\"$(abspath $2)\",\"$(abspath $1)\")")
 
-%manifest: %manifest.template
+%.manifest: %.manifest.template
 	@echo [ $@ ]
 	RELDIR=$(filter-out ./,$(call relative-to,$(dir $@),$(shell pwd))/) && \
 	sed $(manifest_rules) $< > $@
@@ -76,9 +78,9 @@ manifest: manifest.template
 	@echo [ $@ ]
 	sed $(manifest_rules) $< > $@
 
-ifneq ($(MAKECMDGOALS),clean)
+ifeq ($(filter clean,$(MAKECMDGOALS)),)
 ifeq ($(SGX),1)
-include $(addsuffix .manifest.sgx.d,$(exec_target))
+include $(addsuffix .manifest.sgx.d,$(patsubst %.manifest,%,$(exec_target)))
 endif
 endif
 
diff --git a/LibOS/shim/test/apps b/LibOS/shim/test/apps
index 937b59d5..b60c298e 160000
--- a/LibOS/shim/test/apps
+++ b/LibOS/shim/test/apps
@@ -1 +1 @@
-Subproject commit 937b59d5e998ac8ab9e3addb72f5f4a09efda659
+Subproject commit b60c298e4446e0fe38eef963196af28cf012d3b0
diff --git a/LibOS/shim/test/benchmark/Makefile b/LibOS/shim/test/benchmark/Makefile
index 1341a4e8..2db56de0 100644
--- a/LibOS/shim/test/benchmark/Makefile
+++ b/LibOS/shim/test/benchmark/Makefile
@@ -4,8 +4,6 @@ cxx_executables = $(patsubst %.cpp,%,$(wildcard *.cpp))
 target = $(c_executables) $(cxx_executables) \
 	  manifest
 
-include ../../../../Makefile.configs
-include ../../../../Makefile.rules
 include ../Makefile.Test
 
 %.manifest: %.manifest.template
@@ -21,10 +19,10 @@ LDLIBS-rpc_latency.libos += -llibos
 LDLIBS-rpc_latency2.libos += -llibos
 LDLIBS-test_start.m += -lm
 
-%: %.c
+$(c_executables): %: %.c
 	$(call cmd,csingle)
 
-%: %.cpp
+$(cxx_executables): %: %.cpp
 	$(call cmd,cxxsingle)
 else
 .IGNORE: $(c_executables) $(cxx_executables)
diff --git a/LibOS/shim/test/inline/Makefile b/LibOS/shim/test/inline/Makefile
index 31b4cd94..f0c736ac 100644
--- a/LibOS/shim/test/inline/Makefile
+++ b/LibOS/shim/test/inline/Makefile
@@ -7,8 +7,6 @@ target = $(c_executables) $(cxx_executables) manifest
 .PHONY: default
 default: all
 
-include ../../../../Makefile.configs
-include ../../../../Makefile.rules
 include ../Makefile.Test
 
 $(PALDIR)/user_start.o: $(PALDIR)/user_start.S
diff --git a/LibOS/shim/test/native/Makefile b/LibOS/shim/test/native/Makefile
index 9679f676..4fe930dc 100644
--- a/LibOS/shim/test/native/Makefile
+++ b/LibOS/shim/test/native/Makefile
@@ -5,8 +5,6 @@ manifests = $(patsubst %.template,%,$(wildcard *.manifest.template)) manifest
 exec_target = $(c_executables) $(cxx_executables) ls.manifest
 target = $(exec_target) $(manifests)
 
-include ../../../../Makefile.configs
-include ../../../../Makefile.rules
 include ../Makefile.Test
 
 ifeq ($(findstring x86_64,$(SYS))$(findstring linux,$(SYS)),x86_64linux)
@@ -25,10 +23,10 @@ LDLIBS-start.pthread.m += -lpthread -lm
 LDLIBS-sync.pthread += -lpthread
 LDLIBS-test_start_pthread_m.m += -lm
 
-%: %.c
+$(c_executables): %: %.c
 	$(call cmd,csingle)
 
-%: %.cpp
+$(cxx_executables): %: %.cpp
 	$(call cmd,cxxsingle)
 
 include $(wildcard *.d)
diff --git a/LibOS/shim/test/regression/Makefile b/LibOS/shim/test/regression/Makefile
index 5cf19b3f..dd81d667 100644
--- a/LibOS/shim/test/regression/Makefile
+++ b/LibOS/shim/test/regression/Makefile
@@ -10,8 +10,6 @@ clean-extra += clean-tmp
 .PHONY: default
 default: all
 
-include ../../../../Makefile.configs
-include ../../../../Makefile.rules
 include ../Makefile.Test
 
 ifeq ($(findstring x86_64,$(SYS))$(findstring linux,$(SYS)),x86_64linux)