diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 0000000..f26f517
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1 @@
+SUBDIRS = usbboot xbboot
diff --git a/usbboot/autogen.sh b/autogen.sh
similarity index 100%
rename from usbboot/autogen.sh
rename to autogen.sh
diff --git a/usbboot/configure.ac b/configure.ac
similarity index 93%
rename from usbboot/configure.ac
rename to configure.ac
index 9253dd2..fa6c1a3 100644
--- a/usbboot/configure.ac
+++ b/configure.ac
@@ -55,5 +55,7 @@ AC_FUNC_MALLOC
 AC_FUNC_MEMCMP
 AC_CHECK_FUNCS([memset strerror])
 
-AC_CONFIG_FILES(Makefile src/Makefile )
+AC_CONFIG_FILES(Makefile \
+		usbboot/Makefile usbboot/src/Makefile \
+		xbboot/Makefile xbboot/host-app/Makefile)
 AC_OUTPUT
diff --git a/usbboot/Makefile.am b/usbboot/Makefile.am
index 9ce812d..af437a6 100644
--- a/usbboot/Makefile.am
+++ b/usbboot/Makefile.am
@@ -1,2 +1 @@
 SUBDIRS = src
-EXTRA_DIST = autogen.sh
diff --git a/xbboot/Makefile.am b/xbboot/Makefile.am
index 0e307d9..c487b2c 100644
--- a/xbboot/Makefile.am
+++ b/xbboot/Makefile.am
@@ -1,2 +1 @@
 SUBDIRS = host-app
-EXTRA_DIST = autogen.sh
diff --git a/xbboot/autogen.sh b/xbboot/autogen.sh
deleted file mode 100755
index 8701df8..0000000
--- a/xbboot/autogen.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-export AUTOMAKE="automake --foreign --add-missing --copy"
-autoreconf
diff --git a/xbboot/configure.ac b/xbboot/configure.ac
deleted file mode 100644
index 3b31fa1..0000000
--- a/xbboot/configure.ac
+++ /dev/null
@@ -1,56 +0,0 @@
-#
-# autoconf configuration for xbboot
-#
-
-AC_PREREQ(2.63)
-AC_INIT([xbboot], [0.1])
-AC_CONFIG_AUX_DIR(m4)
-AM_INIT_AUTOMAKE(AC_PACKAGE_NAME, AC_PACKAGE_VERSION)
-AM_CONFIG_HEADER([config.h])
-
-AM_MAINTAINER_MODE
-
-AC_ARG_ENABLE([firmware],
- [AS_HELP_STRING([--disable-firmware],
-  [Do not build initialization code]
-  [(for example, because some other package contains it).])],
- [
-case "$enableval" in
-yes) firmware=true ;;
-no) firmware=false ;;
-*) AC_MSG_ERROR([bad value $enableval for --enable-firmware]) ;;
-esac],[firmware=false])
-AM_CONDITIONAL([COND_FIRMWARE], [test "$firmware" = true])
-
-# Checks for programs.
-AC_PROG_CC
-AC_PROG_CXX
-
-# Checks for libraries.
-AC_CHECK_LIB([c], [main])
-AC_CHECK_LIB([gcc], [main])
-AC_CHECK_LIB([m], [main])
-AC_CHECK_LIB([usb], [main], [], [
-echo "Error! You need to have libusb-dev.\n"
-echo "Maybe run 'sudo apt-get install libusb-dev' under debian"
-exit -1 ])
-
-LIBS="$LIBS $USB_LIBS"
-CFLAGS="$CFLAGS $USB_CFLAGS"
-
-# Checks for header files.
-AC_HEADER_STDC
-AC_CHECK_HEADERS([time.h stdlib.h string.h])
-
-# Checks for typedefs, structures, and compiler characteristics.
-AC_C_INLINE
-AC_TYPE_SIZE_T
-AC_TYPE_UINT8_T
-
-# Checks for library functions.
-AC_FUNC_MALLOC
-AC_FUNC_MEMCMP
-AC_CHECK_FUNCS([memset strerror])
-
-AC_CONFIG_FILES(Makefile host-app/Makefile)
-AC_OUTPUT
diff --git a/xbboot/host-app/Makefile.am b/xbboot/host-app/Makefile.am
index 8226063..4348942 100644
--- a/xbboot/host-app/Makefile.am
+++ b/xbboot/host-app/Makefile.am
@@ -9,7 +9,6 @@ BUILT_SOURCES = xbboot_version.h
 bin_PROGRAMS = xbboot
 xbboot_SOURCES = host_main.c
 
-prefix = /usr
 pkgdatadir = $(datadir)/xburst-tools/
 
 if COND_FIRMWARE