diff --git a/Makefile b/Makefile
index 3f34ef7104..43a4333cf1 100644
--- a/Makefile
+++ b/Makefile
@@ -131,7 +131,7 @@ endif
 #
 .PHONY:	clean
 clean:
-	@make -C $(NUTTX_SRC) -r $(MQUIET) clean
+	@make -C $(NUTTX_SRC) -r $(MQUIET) distclean
 	@make -C $(ROMFS_SRC) -r $(MQUIET) clean
 
 .PHONY:	distclean
diff --git a/apps/px4/px4io/driver/px4io.cpp b/apps/px4/px4io/driver/px4io.cpp
index fafec77f90..a5def874d8 100644
--- a/apps/px4/px4io/driver/px4io.cpp
+++ b/apps/px4/px4io/driver/px4io.cpp
@@ -65,7 +65,7 @@
 #include <systemlib/perf_counter.h>
 #include <systemlib/hx_stream.h>
 
-#include "../protocol.h"
+#include "px4io/protocol.h"
 #include "uploader.h"
 
 class PX4IO;
diff --git a/apps/px4/px4io/protocol.h b/apps/px4/px4io/protocol.h
deleted file mode 100644
index c186c5b862..0000000000
--- a/apps/px4/px4io/protocol.h
+++ /dev/null
@@ -1,73 +0,0 @@
-/****************************************************************************
- *
- *   Copyright (C) 2012 PX4 Development Team. All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *
- * 1. Redistributions of source code must retain the above copyright
- *    notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- *    notice, this list of conditions and the following disclaimer in
- *    the documentation and/or other materials provided with the
- *    distribution.
- * 3. Neither the name PX4 nor the names of its contributors may be
- *    used to endorse or promote products derived from this software
- *    without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- * COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- * OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
- * AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- *
- ****************************************************************************/
-
-/**
- * @file PX4FMU <-> PX4IO messaging protocol.
- *
- * This initial version of the protocol is very simple; each side transmits a
- * complete update with each frame.  This avoids the sending of many small
- * messages and the corresponding complexity involved.
- */
-
-/*
- * XXX MUST BE KEPT IN SYNC WITH THE VERSION IN PX4FMU UNTIL
- * TREES ARE MERGED.
- */
-
-#define PX4IO_OUTPUT_CHANNELS	8
-#define PX4IO_INPUT_CHANNELS	12
-#define PX4IO_RELAY_CHANNELS	2
-
-#pragma pack(push,1)
-
-/* command from FMU to IO */
-struct px4io_command {
-	uint16_t	f2i_magic;
-#define F2I_MAGIC	0x636d
-
-	uint16_t	servo_command[PX4IO_OUTPUT_CHANNELS];
-	bool		relay_state[PX4IO_RELAY_CHANNELS];
-	bool		arm_ok;
-};
-
-/* report from IO to FMU */
-struct px4io_report {
-	uint16_t	i2f_magic;
-#define I2F_MAGIC		0x7570
-
-	uint16_t	rc_channel[PX4IO_INPUT_CHANNELS];
-	bool		armed;
-	uint8_t		channel_count;
-} __attribute__((packed));
-
-#pragma pack(pop)
diff --git a/apps/px4io/Makefile b/apps/px4io/Makefile
index 06be90a0ce..9b63d3ac80 100644
--- a/apps/px4io/Makefile
+++ b/apps/px4io/Makefile
@@ -35,4 +35,15 @@
 # Build the px4io application.
 #
 
+#
+# Note that we pull a couple of specific files from the systemlib, since
+# we can't support it all.
+#
+CSRCS	= comms.c \
+	  mixer.c \
+	  px4io.c \
+	  safety.c \
+	  ../systemlib/hx_stream.c \
+	  ../systemlib/perf_counter.c
+
 include $(APPDIR)/mk/app.mk
diff --git a/apps/px4io/protocol.h b/apps/px4io/protocol.h
index 92558a61df..96e0ca3500 100644
--- a/apps/px4io/protocol.h
+++ b/apps/px4io/protocol.h
@@ -48,6 +48,8 @@
 #define PX4IO_INPUT_CHANNELS	12
 #define PX4IO_RELAY_CHANNELS	2
 
+#pragma pack(push, 1)
+
 /* command from FMU to IO */
 struct px4io_command {
 	uint16_t	f2i_magic;
@@ -56,7 +58,7 @@ struct px4io_command {
 	uint16_t	servo_command[PX4IO_OUTPUT_CHANNELS];
 	bool		relay_state[PX4IO_RELAY_CHANNELS];
 	bool		arm_ok;
-} __attribute__((packed));
+};
 
 /* report from IO to FMU */
 struct px4io_report {
@@ -66,4 +68,6 @@ struct px4io_report {
 	uint16_t	rc_channel[PX4IO_INPUT_CHANNELS];
 	bool		armed;
 	uint8_t		channel_count;
-} __attribute__((packed));
+};
+
+#pragma pack(pop)
\ No newline at end of file
diff --git a/apps/systemlib/err.c b/apps/systemlib/err.c
index 8f76aabe9b..9692f03dd9 100644
--- a/apps/systemlib/err.c
+++ b/apps/systemlib/err.c
@@ -38,7 +38,8 @@
  * the same names.
  */
 
-#include <stdio.h>
+#include <nuttx/config.h>
+
 #include <stdlib.h>
 #include <errno.h>
 #include <string.h>
@@ -47,17 +48,31 @@
 
 #define NOCODE		1000	/* larger than maximum errno */
 
+#if CONFIG_NFILE_STREAMS > 0
+#  include <stdio.h>
+#elif defined(CONFIG_ARCH_LOWPUTC)
+#  include <debug.h>
+extern int lib_lowvprintf(const char *fmt, va_list ap);
+#else
+#  warning Cannot output without one of CONFIG_NFILE_STREAMS or CONFIG_ARCH_LOWPUTC
+#endif
+
 const char *
 getprogname(void)
 {
+#if CONFIG_TASK_NAME_SIZE > 0
 	_TCB	*thisproc = sched_self();
 
 	return thisproc->name;
+#else
+	return "app";
+#endif
 }
 
 static void
 warnerr_core(int errcode, const char *fmt, va_list args)
 {
+#if CONFIG_NFILE_STREAMS > 0
 	fprintf(stderr, "%s: ", getprogname());
 	vfprintf(stderr, fmt, args);
 
@@ -67,6 +82,17 @@ warnerr_core(int errcode, const char *fmt, va_list args)
 	if (errcode < NOCODE)
 		fprintf(stderr, ": %s", strerror(errcode));
 	fprintf(stderr, "\n");
+#elif CONFIG_ARCH_LOWPUTC
+	lib_lowprintf("%s: ", getprogname());
+	lib_lowvprintf(fmt, args);
+
+	/* convenience as many parts of NuttX use negative errno */
+	if (errcode < 0)
+		errcode = -errcode;
+	if (errcode < NOCODE)
+		lib_lowprintf(": %s", strerror(errcode));
+	lib_lowprintf("\n");
+#endif
 }
 
 void
diff --git a/nuttx/configs/px4io/io/appconfig b/nuttx/configs/px4io/io/appconfig
index 94176c6dcf..fbe8307a70 100644
--- a/nuttx/configs/px4io/io/appconfig
+++ b/nuttx/configs/px4io/io/appconfig
@@ -1,8 +1,6 @@
 ############################################################################
-# configs/stm3210e-eval/nsh/appconfig
 #
-#   Copyright (C) 2011-2012 Gregory Nutt. All rights reserved.
-#   Author: Gregory Nutt <gnutt@nuttx.org>
+#   Copyright (C) 2012 PX4 Development Team. All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
 # modification, are permitted provided that the following conditions
@@ -14,7 +12,7 @@
 #    notice, this list of conditions and the following disclaimer in
 #    the documentation and/or other materials provided with the
 #    distribution.
-# 3. Neither the name NuttX nor the names of its contributors may be
+# 3. Neither the name PX4 nor the names of its contributors may be
 #    used to endorse or promote products derived from this software
 #    without specific prior written permission.
 #
@@ -33,7 +31,4 @@
 #
 ############################################################################
 
-# Path to px4io app containing the user_start entry point
-
 CONFIGURED_APPS += px4io
-CONFIGURED_APPS += systemlib