diff --git a/Make.inc b/Make.inc
index 3bceb7bf8adb8..568582c425d06 100644
--- a/Make.inc
+++ b/Make.inc
@@ -177,7 +177,7 @@ endif
 USE_GPL_LIBS ?= 1
 
 # Directories where said libraries get installed to
-prefix ?= $(abspath julia-$(JULIA_COMMIT))
+prefix ?= $(BUILDROOT)/julia-$(JULIA_COMMIT)
 bindir := $(prefix)/bin
 libdir := $(prefix)/lib
 libexecdir := $(prefix)/libexec
diff --git a/Makefile b/Makefile
index 846b252996923..337643c272bb7 100644
--- a/Makefile
+++ b/Makefile
@@ -21,7 +21,7 @@ all: debug release
 # sort is used to remove potential duplicates
 DIRS := $(sort $(build_bindir) $(build_depsbindir) $(build_libdir) $(build_private_libdir) $(build_libexecdir) $(build_includedir) $(build_includedir)/julia $(build_sysconfdir)/julia $(build_datarootdir)/julia $(build_man1dir))
 ifneq ($(BUILDROOT),$(JULIAHOME))
-BUILDDIRS := $(BUILDROOT) $(addprefix $(BUILDROOT)/,base src ui doc deps test test/perf)
+BUILDDIRS := $(BUILDROOT) $(addprefix $(BUILDROOT)/,base src ui doc deps test test/perf examples examples/embedding)
 BUILDDIRMAKE := $(addsuffix /Makefile,$(BUILDDIRS))
 DIRS := $(DIRS) $(BUILDDIRS)
 $(BUILDDIRMAKE): | $(BUILDDIRS)
@@ -339,16 +339,15 @@ install: $(build_depsbindir)/stringreplace $(BUILDROOT)/doc/_build/html/en/index
 	done
 
 	$(INSTALL_M) $(build_bindir)/julia* $(DESTDIR)$(bindir)/
+	-cp -a $(build_libexecdir) $(DESTDIR)$(prefix)
 ifeq ($(OS),WINNT)
 	-$(INSTALL_M) $(build_bindir)/*.dll $(DESTDIR)$(bindir)/
 	-$(INSTALL_M) $(build_libdir)/libjulia.dll.a $(DESTDIR)$(libdir)/
 	-$(INSTALL_M) $(build_libdir)/libjulia-debug.dll.a $(DESTDIR)$(libdir)/
 	-$(INSTALL_M) $(build_bindir)/libopenlibm.dll.a $(DESTDIR)$(libdir)/
 else
-	-cp -a $(build_libexecdir) $(DESTDIR)$(prefix)
-
-	# Copy over .dSYM directories directly
 ifeq ($(OS),Darwin)
+	# Copy over .dSYM directories directly
 	-cp -a $(build_libdir)/*.dSYM $(DESTDIR)$(libdir)
 	-cp -a $(build_private_libdir)/*.dSYM $(DESTDIR)$(private_libdir)
 endif
diff --git a/appveyor.yml b/appveyor.yml
index e8cec32f6c96b..e2f7543300df3 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -55,5 +55,5 @@ build_script:
 test_script:
   - usr\bin\julia -e "versioninfo()"
   - usr\bin\julia --precompiled=no -e "true"
-  - cd test && ..\usr\bin\julia --check-bounds=yes runtests.jl all &&
-      ..\usr\bin\julia --check-bounds=yes runtests.jl libgit2-online download pkg embedding
+  - cd julia-* && .\bin\julia.exe --check-bounds=yes share\julia\test\runtests.jl all &&
+      .\bin\julia.exe --check-bounds=yes share\julia\test\runtests.jl libgit2-online download pkg embedding
diff --git a/contrib/windows/msys_build.sh b/contrib/windows/msys_build.sh
index f9c3c08aedba6..500171f72c4d7 100755
--- a/contrib/windows/msys_build.sh
+++ b/contrib/windows/msys_build.sh
@@ -203,7 +203,7 @@ fi
 echo 'FORCE_ASSERTIONS = 1' >> Make.user
 
 cat Make.user
-make -j3 VERBOSE=1
+make -j3 VERBOSE=1 install
+cp usr/bin/busybox.exe julia-*/bin
 make build-stats
-#make debug
 make VERBOSE=1 -C examples
diff --git a/examples/Makefile b/examples/Makefile
index f1950b7d2f6a4..bc065d751530b 100644
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -1,7 +1,6 @@
 SRCDIR := $(abspath $(dir $(lastword $(MAKEFILE_LIST))))
 BUILDDIR := .
 JULIAHOME := $(abspath $(SRCDIR)/..)
-prefix := $(JULIAHOME)/usr
 include $(JULIAHOME)/Make.inc
 
 outdir := $(libexecdir)
diff --git a/examples/embedding/Makefile b/examples/embedding/Makefile
index 4ad51f5ce46d8..c5710924abbb8 100644
--- a/examples/embedding/Makefile
+++ b/examples/embedding/Makefile
@@ -11,6 +11,9 @@ ifndef BIN
 endif
 
 #=============================================================================
+# this source directory where embedding.c is located
+SRCDIR := $(abspath $(dir $(lastword $(MAKEFILE_LIST))))
+
 # get the executable suffix, if any
 EXE := $(suffix $(abspath $(JULIA)))
 
@@ -26,10 +29,10 @@ DEBUGFLAGS += -g
 release: $(BIN)/embedding$(EXE)
 debug:   $(BIN)/embedding-debug$(EXE)
 
-$(BIN)/embedding$(EXE): embedding.c
+$(BIN)/embedding$(EXE): $(SRCDIR)/embedding.c
 	$(CC) $^ -o $@ $(CFLAGS)
 
-$(BIN)/embedding-debug$(EXE): embedding.c
+$(BIN)/embedding-debug$(EXE): $(SRCDIR)/embedding.c
 	$(CC) $^ -o $@ $(CFLAGS) $(DEBUGFLAGS)
 
 clean: