diff --git a/apps/Makefile b/apps/Makefile
index 826694dad4..77f2012ef8 100644
--- a/apps/Makefile
+++ b/apps/Makefile
@@ -35,7 +35,6 @@
 ############################################################################
 
 -include $(TOPDIR)/Make.defs
--include $(TOPDIR)/.config
 
 APPDIR = ${shell pwd}
 
diff --git a/apps/examples/Makefile b/apps/examples/Makefile
index 269d2b4643..2bff9934e6 100644
--- a/apps/examples/Makefile
+++ b/apps/examples/Makefile
@@ -104,13 +104,13 @@ all: nothing
 
 define SDIR_template
 $(1)_$(2):
-	$(MAKE) -C $(1) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
+	$(MAKE) -C $(1) $(2) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
 endef
 
 $(foreach SDIR, $(CNTXTDIRS), $(eval $(call SDIR_template,$(SDIR),context)))
 $(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),depend)))
 $(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),clean)))
-$(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),disclean)))
+$(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),distclean)))
 
 nothing:
 
diff --git a/apps/examples/cxxtest/Makefile b/apps/examples/cxxtest/Makefile
index e6bdd34fc3..b0f0befbf0 100644
--- a/apps/examples/cxxtest/Makefile
+++ b/apps/examples/cxxtest/Makefile
@@ -73,7 +73,7 @@ STACKSIZE	= 4096
 VPATH		= 
 
 all: .built
-.PHONY:	clean depend disclean chkcxx
+.PHONY:	clean depend distclean chkcxx
 
 chkcxx:
 ifneq ($(CONFIG_HAVE_CXX),y)
diff --git a/apps/examples/elf/Makefile b/apps/examples/elf/Makefile
index 24472139fb..8831a9336e 100644
--- a/apps/examples/elf/Makefile
+++ b/apps/examples/elf/Makefile
@@ -65,7 +65,7 @@ ROOTDEPPATH	= --dep-path . --dep-path tests
 VPATH = tests
 
 all: .built
-.PHONY: really_build clean_tests clean depend disclean
+.PHONY: really_build clean_tests clean depend distclean
 
 $(AOBJS): %$(OBJEXT): %.S
 	$(call ASSEMBLE, $<, $@)
diff --git a/apps/examples/helloxx/Makefile b/apps/examples/helloxx/Makefile
index fd126d345f..295d0116e7 100644
--- a/apps/examples/helloxx/Makefile
+++ b/apps/examples/helloxx/Makefile
@@ -73,7 +73,7 @@ STACKSIZE	= 2048
 VPATH		= 
 
 all: .built
-.PHONY:	clean depend disclean chkcxx
+.PHONY:	clean depend distclean chkcxx
 
 chkcxx:
 ifneq ($(CONFIG_HAVE_CXX),y)
diff --git a/apps/examples/nettest/Makefile b/apps/examples/nettest/Makefile
index 75e4cf0bea..c1c50bbb8f 100644
--- a/apps/examples/nettest/Makefile
+++ b/apps/examples/nettest/Makefile
@@ -96,7 +96,7 @@ STACKSIZE	= 2048
 VPATH		= 
 
 all: .built $(HOST_BIN)
-.PHONY:	clean depend disclean
+.PHONY:	clean depend distclean
 
 $(TARG_AOBJS): %$(OBJEXT): %.S
 	$(call ASSEMBLE, $<, $@)
diff --git a/apps/examples/nxflat/Makefile b/apps/examples/nxflat/Makefile
index 07c163347d..4fc315592c 100644
--- a/apps/examples/nxflat/Makefile
+++ b/apps/examples/nxflat/Makefile
@@ -65,7 +65,7 @@ ROOTDEPPATH	= --dep-path .
 VPATH		= 
 
 all: .built
-.PHONY: headers clean depend disclean
+.PHONY: headers clean depend distclean
 
 $(AOBJS): %$(OBJEXT): %.S
 	$(call ASSEMBLE, $<, $@)
diff --git a/apps/examples/romfs/Makefile b/apps/examples/romfs/Makefile
index b247db6f62..3701412762 100644
--- a/apps/examples/romfs/Makefile
+++ b/apps/examples/romfs/Makefile
@@ -65,7 +65,7 @@ ROOTDEPPATH	= --dep-path .
 VPATH		= 
 
 all: .built
-.PHONY:	checkgenromfs clean depend disclean
+.PHONY:	checkgenromfs clean depend distclean
 
 $(AOBJS): %$(OBJEXT): %.S
 	$(call ASSEMBLE, $<, $@)
diff --git a/apps/examples/udp/Makefile b/apps/examples/udp/Makefile
index 6bfdce9cc1..d6c89cac44 100644
--- a/apps/examples/udp/Makefile
+++ b/apps/examples/udp/Makefile
@@ -87,7 +87,7 @@ ROOTDEPPATH	= --dep-path .
 VPATH		= 
 
 all: .built
-.PHONY:	clean depend disclean
+.PHONY:	clean depend distclean
 
 $(TARG_AOBJS): %$(OBJEXT): %.S
 	$(call ASSEMBLE, $<, $@)
diff --git a/apps/graphics/Makefile b/apps/graphics/Makefile
index bebb31b5a6..474118450b 100644
--- a/apps/graphics/Makefile
+++ b/apps/graphics/Makefile
@@ -48,13 +48,13 @@ all: nothing
 
 define SDIR_template
 $(1)_$(2):
-	$(MAKE) -C $(1) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
+	$(MAKE) -C $(1) $(2) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
 endef
 
 $(foreach SDIR, $(CNTXTDIRS), $(eval $(call SDIR_template,$(SDIR),context)))
 $(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),depend)))
 $(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),clean)))
-$(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),disclean)))
+$(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),distclean)))
 
 nothing:
 
diff --git a/apps/interpreters/Makefile b/apps/interpreters/Makefile
index 1eeab585e0..3569a0044a 100644
--- a/apps/interpreters/Makefile
+++ b/apps/interpreters/Makefile
@@ -52,12 +52,12 @@ all: nothing
 
 define SDIR_template
 $(1)_$(2):
-	$(MAKE) -C $(1) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
+	$(MAKE) -C $(1) $(2) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
 endef
 
 $(foreach SDIR, $(INSTALLED_DIRS), $(eval $(call SDIR_template,$(SDIR),depend)))
 $(foreach SDIR, $(INSTALLED_DIRS), $(eval $(call SDIR_template,$(SDIR),clean)))
-$(foreach SDIR, $(INSTALLED_DIRS), $(eval $(call SDIR_template,$(SDIR),disclean)))
+$(foreach SDIR, $(INSTALLED_DIRS), $(eval $(call SDIR_template,$(SDIR),distclean)))
 
 nothing:
 
diff --git a/apps/netutils/Makefile b/apps/netutils/Makefile
index 303b804b6c..b557c73cc8 100644
--- a/apps/netutils/Makefile
+++ b/apps/netutils/Makefile
@@ -49,12 +49,12 @@ all: nothing
 
 define SDIR_template
 $(1)_$(2):
-	$(MAKE) -C $(1) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
+	$(MAKE) -C $(1) $(2) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
 endef
 
 $(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),depend)))
 $(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),clean)))
-$(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),disclean)))
+$(foreach SDIR, $(SUBDIRS), $(eval $(call SDIR_template,$(SDIR),distclean)))
 
 nothing:
 
diff --git a/apps/system/Makefile b/apps/system/Makefile
index 572598e398..c59059d811 100644
--- a/apps/system/Makefile
+++ b/apps/system/Makefile
@@ -41,9 +41,15 @@ SUBDIRS = free i2c install readline poweroff ramtron sdcard sysinfo
 
 # Create the list of installed runtime modules (INSTALLED_DIRS)
 
+ifeq ($(CONFIG_WINDOWS_NATIVE),y)
 define ADD_DIRECTORY
-INSTALLED_DIRS  += ${shell if [ -r $1/Makefile ]; then echo "$1"; fi}
+  INSTALLED_DIRS  += $(if $(wildcard .\$1\Makefile),$1,)
 endef
+else
+define ADD_DIRECTORY
+  INSTALLED_DIRS  += $(if $(wildcard ./$1/Makefile),$1,)
+endef
+endif
 
 $(foreach DIR, $(SUBDIRS), $(eval $(call ADD_DIRECTORY,$(DIR))))
 
@@ -52,12 +58,12 @@ all: nothing
 
 define SDIR_template
 $(1)_$(2):
-	$(MAKE) -C $(1) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
+	$(MAKE) -C $(1) $(2) TOPDIR="$(TOPDIR)" APPDIR="$(APPDIR)"
 endef
 
 $(foreach SDIR, $(INSTALLED_DIRS), $(eval $(call SDIR_template,$(SDIR),depend)))
 $(foreach SDIR, $(INSTALLED_DIRS), $(eval $(call SDIR_template,$(SDIR),clean)))
-$(foreach SDIR, $(INSTALLED_DIRS), $(eval $(call SDIR_template,$(SDIR),disclean)))
+$(foreach SDIR, $(INSTALLED_DIRS), $(eval $(call SDIR_template,$(SDIR),distclean)))
 
 nothing:
 
diff --git a/nuttx/tools/Config.mk b/nuttx/tools/Config.mk
index b7f8d9bbe0..f05933f1ab 100644
--- a/nuttx/tools/Config.mk
+++ b/nuttx/tools/Config.mk
@@ -154,10 +154,12 @@ define ARCHIVE
 endef
 endif
 
-define CLEAN
 ifeq ($(CONFIG_WINDOWS_NATIVE),y)
+define CLEAN
 	$(Q) rm -f *.o *.a
-else
-	$(Q) rm -f *.o *.a *~ .*.swp
-endif
 endef
+else
+define CLEAN
+	$(Q) rm -f *.o *.a *~ .*.swp
+endef
+endif