diff --git a/Makefile b/Makefile
index 22102a91bf..9c20f4f26d 100644
--- a/Makefile
+++ b/Makefile
@@ -80,6 +80,7 @@ ADDON_DIRS	:= $(PCODE_DIR) $(NX_DIR) $(APPDIR)
 
 NONFSDIRS	= sched lib $(ARCH_SRC) mm $(ADDON_DIRS)
 FSDIRS		= fs drivers binfmt
+NETFSDIRS	= fs drivers
 CONTEXTDIRS	=
 
 ifeq ($(CONFIG_NX),y)
@@ -98,17 +99,26 @@ endif
 CLEANDIRS	= $(NONFSDIRS) $(FSDIRS)
 MAKEDIRS	= $(NONFSDIRS)
 
+# Add file system directories to MAKEDIRS (they are already in CLEANDIRS)
+
 ifeq ($(CONFIG_NFILE_DESCRIPTORS),0)
+ifeq ($(CONFIG_NET),y)
 ifneq ($(CONFIG_NSOCKET_DESCRIPTORS),0)
 MAKEDIRS	+= fs
 endif
-ifeq ($(CONFIG_NET),y)
-MAKEDIRS	+= net
+MAKEDIRS	+= drivers
 endif
 else
 MAKEDIRS	+= $(FSDIRS)
 endif
 
+# Add networking directories to MAKEDIRS and CLEANDIRS
+
+ifeq ($(CONFIG_NET),y)
+MAKEDIRS	+= net
+endif
+CLEANDIRS	+= net
+
 #
 # Extra objects used in the final link.
 #
@@ -367,7 +377,8 @@ subdir_distclean:
 	done
 
 distclean: clean subdir_distclean clean_context
-	@rm -f Make.defs setenv.sh .config
 ifeq ($(CONFIG_BUILD_2PASS),y)
 	@$(MAKE) -C $(CONFIG_PASS1_BUILDIR) TOPDIR="$(TOPDIR)" distclean
 endif
+	@rm -f Make.defs setenv.sh .config
+
diff --git a/configs/README.txt b/configs/README.txt
index ca14c42244..f7891dd08a 100644
--- a/configs/README.txt
+++ b/configs/README.txt
@@ -171,12 +171,9 @@ defconfig -- This is a configuration file similar to the Linux
 		CONFIG_APP_DIR - Identifies the directory that builds the
 		  application to link with NuttX. This symbol must be assigned
 		  to the path to the application build directory *relative* to
-		  the NuttX top build direcory. As an an example, there are
-		  several example applicatins in the NuttX examples/ sub-directory.
-                  To use one of these example applications, say nsh, you would
-		  set CONFIG_APP_DIR=examples/nsh. If you had an application
-		  directory and the NuttX directory both within another directory
-		  like this:
+		  the NuttX top build direcory. If you had an application
+          directory and the NuttX directory each in separate directory
+		  trees like this:
 
 		  build
 		   |-nuttx
@@ -202,7 +199,7 @@ defconfig -- This is a configuration file similar to the Linux
 		    This is only done when you change the NuttX configuration.
 		  - depend. Make or update the application build dependencies.
 
-		  When this application is invoked it will receive the setting TOPDIR< like:
+		  When this application is invoked it will receive the setting TOPDIR like:
 
 		    $(MAKE) -C $(CONFIG_APP_DIR) TOPDIR="$(TOPDIR)" <target>
 
diff --git a/configs/ea3131/locked/Makefile b/configs/ea3131/locked/Makefile
index 26a62a683c..a6bae11a06 100755
--- a/configs/ea3131/locked/Makefile
+++ b/configs/ea3131/locked/Makefile
@@ -41,7 +41,16 @@
 PASS1_SRCDIR	= arch/$(CONFIG_ARCH)/src
 PASS1_BOARDDIR	= $(PASS1_SRCDIR)/board
 PASS1_LIBBOARD	= $(PASS1_BOARDDIR)/libboard$(LIBEXT)
+
+# Where is the application library?
+
+ifneq ($(CONFIG_APP_DIR),)
 PASS1_LIBAPP	= $(CONFIG_APP_DIR)/libapp$(LIBEXT)
+else
+ifneq ($(APPDIR),)
+PASS1_LIBAPP	= $(APPDIR)/libapps$(LIBEXT)
+endif
+endif
 
 # Remove the application library (libapp) from the list of libraries.  Add
 # the boad library (liboard)
diff --git a/configs/ea3131/src/Makefile b/configs/ea3131/src/Makefile
index cb3cc3da8d..c97c4fecf0 100755
--- a/configs/ea3131/src/Makefile
+++ b/configs/ea3131/src/Makefile
@@ -59,7 +59,7 @@ endif
 ifeq ($(CONFIG_PAGING),y)
 CSRCS		+= up_fillpage.c
 endif
-ifeq ($(CONFIG_APP_DIR),examples/usbstorage)
+ifeq ($(CONFIG_USBSTRG),y)
 CSRCS		+= up_usbstrg.c
 endif
 COBJS		= $(CSRCS:.c=$(OBJEXT))
diff --git a/configs/mbed/src/Makefile b/configs/mbed/src/Makefile
index 98b824b66b..876f77b7df 100755
--- a/configs/mbed/src/Makefile
+++ b/configs/mbed/src/Makefile
@@ -42,7 +42,7 @@ CSRCS		= up_boot.c up_leds.c
 ifeq ($(CONFIG_NSH_ARCHINIT),y)
 CSRCS		+= up_nsh.c
 endif
-ifeq ($(CONFIG_APP_DIR),examples/usbstorage)
+ifeq ($(CONFIG_USBSTRG),y)
 CSRCS		+= up_usbstrg.c
 endif
 
diff --git a/configs/mcu123-lpc214x/src/Makefile b/configs/mcu123-lpc214x/src/Makefile
index e3f86453fd..a69beca5a0 100644
--- a/configs/mcu123-lpc214x/src/Makefile
+++ b/configs/mcu123-lpc214x/src/Makefile
@@ -51,7 +51,7 @@ CSRCS		= up_spi.c up_leds.c
 ifeq ($(CONFIG_NSH_ARCHINIT),y)
 CSRCS		+= up_nsh.c
 endif
-ifeq ($(CONFIG_APP_DIR),examples/usbstorage)
+ifeq ($(CONFIG_USBSTRG),y)
 CSRCS		+= up_usbstrg.c
 endif
 
diff --git a/configs/nucleus2g/src/Makefile b/configs/nucleus2g/src/Makefile
index 36415136d1..7aca7b05e6 100755
--- a/configs/nucleus2g/src/Makefile
+++ b/configs/nucleus2g/src/Makefile
@@ -42,7 +42,7 @@ CSRCS		= up_boot.c up_leds.c up_ssp.c
 ifeq ($(CONFIG_NSH_ARCHINIT),y)
 CSRCS		+= up_nsh.c
 endif
-ifeq ($(CONFIG_APP_DIR),examples/usbstorage)
+ifeq ($(CONFIG_USBSTRG),y)
 CSRCS		+= up_usbstrg.c
 endif
 
diff --git a/configs/olimex-lpc1766stk/src/Makefile b/configs/olimex-lpc1766stk/src/Makefile
index ae53d08079..6898aac068 100755
--- a/configs/olimex-lpc1766stk/src/Makefile
+++ b/configs/olimex-lpc1766stk/src/Makefile
@@ -42,7 +42,7 @@ CSRCS		= up_boot.c up_leds.c up_ssp.c
 ifeq ($(CONFIG_NSH_ARCHINIT),y)
 CSRCS		+= up_nsh.c
 endif
-ifeq ($(CONFIG_APP_DIR),examples/usbstorage)
+ifeq ($(CONFIG_USBSTRG),y)
 CSRCS		+= up_usbstrg.c
 endif
 ifeq ($(CONFIG_NX_LCDDRIVER),y)
diff --git a/configs/sam3u-ek/src/Makefile b/configs/sam3u-ek/src/Makefile
index 9aa681b8b4..d40fd39269 100755
--- a/configs/sam3u-ek/src/Makefile
+++ b/configs/sam3u-ek/src/Makefile
@@ -47,7 +47,7 @@ endif
 ifeq ($(CONFIG_SAM3U_HSMCI),y)
 CSRCS		+= up_mmcsd.c
 endif
-ifeq ($(CONFIG_APP_DIR),examples/usbstorage)
+ifeq ($(CONFIG_USBSTRG),y)
 CSRCS		+= up_usbstrg.c
 endif
 COBJS		= $(CSRCS:.c=$(OBJEXT))
diff --git a/configs/sim/nx/defconfig-x11 b/configs/sim/nx/defconfig-x11
index 5d483ef0a2..d01f545228 100644
--- a/configs/sim/nx/defconfig-x11
+++ b/configs/sim/nx/defconfig-x11
@@ -121,7 +121,7 @@ CONFIG_SIM_FBBPP=32
 #   desciptors by task_create() when a new task is started. If
 #   set, all sockets will appear to be closed in the new task.
 #
-CONFIG_APP_DIR=examples/nx
+#CONFIG_APP_DIR=
 CONFIG_DEBUG=y
 CONFIG_DEBUG_VERBOSE=y
 CONFIG_DEBUG_SYMBOLS=n
diff --git a/configs/stm3210e-eval/src/Makefile b/configs/stm3210e-eval/src/Makefile
index 42839b0f47..09f0c518f4 100755
--- a/configs/stm3210e-eval/src/Makefile
+++ b/configs/stm3210e-eval/src/Makefile
@@ -46,7 +46,7 @@ CSRCS		= up_boot.c up_leds.c up_buttons.c up_spi.c up_usbdev.c \
 ifeq ($(CONFIG_NSH_ARCHINIT),y)
 CSRCS		+= up_nsh.c
 endif
-ifeq ($(CONFIG_APP_DIR),examples/usbstorage)
+ifeq ($(CONFIG_USBSTRG),y)
 CSRCS		+= up_usbstrg.c
 endif
 COBJS		= $(CSRCS:.c=$(OBJEXT))
diff --git a/configs/vsn/src/Makefile b/configs/vsn/src/Makefile
index 6e55c30ca0..8b00da4a7a 100644
--- a/configs/vsn/src/Makefile
+++ b/configs/vsn/src/Makefile
@@ -49,7 +49,7 @@ CSRCS		= sysclock.c boot.c leds.c buttons.c spi.c \
 ifeq ($(CONFIG_NSH_ARCHINIT),y)
 CSRCS		+= nsh.c
 endif
-ifeq ($(CONFIG_APP_DIR),examples/usbstorage)
+ifeq ($(CONFIG_USBSTRG),y)
 CSRCS		+= usbstrg.c
 endif
 COBJS		= $(CSRCS:.c=$(OBJEXT))
diff --git a/tools/zipme.sh b/tools/zipme.sh
index c92f6b64e0..7c08bd2714 100755
--- a/tools/zipme.sh
+++ b/tools/zipme.sh
@@ -132,6 +132,10 @@ if [ -f ${ZIP_NAME} ] ; then
       { echo "rm ${ZIP_NAME} failed!" ; exit 1 ; }
 fi
 
+# Write a version file
+
+echo "CONFIG_NUTTX_VERSION=\"${VERSION}\" >${NUTTX}/.version
+
 # Then zip it
 
 ${TAR} ${TAR_NAME} nuttx-${VERSION}/nuttx nuttx-${VERSION}/apps || \