diff --git a/Makefile.am b/Makefile.am
index 03b945c..4dcbb92 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -28,7 +28,7 @@ EXTRA_DIST += \
 	usrp.iss.in \
 	usrp.inf
 
-SUBDIRS = host fpga
+SUBDIRS = host fpga doc firmware
 
 pkgconfigdir = $(libdir)/pkgconfig
 pkgconfig_DATA = \
diff --git a/Makefile.common b/Makefile.common
index 5b99f08..1892fd3 100644
--- a/Makefile.common
+++ b/Makefile.common
@@ -96,11 +96,11 @@ VOLK_LA = @volk_LA@
 
 # How to link in the USRP library from inside the tree
 USRP_INCLUDES = \
-	-I$(abs_top_srcdir)/host/include \
-	-I$(abs_top_builddir)/host/include \
-	-I$(abs_top_srcdir)/firmware/include \
+	-I$(top_srcdir)/host/include \
+	-I$(top_builddir)/host/include \
+	-I$(top_srcdir)/firmware/include \
 	$(NULL)
-USRP_LA = $(abs_top_builddir)/host/lib/libusrp.la
+USRP_LA = $(top_builddir)/host/lib/libusrp.la
 
 # How to link the gcell library from inside the tree (the PPU part)
 GCELL_INCLUDES = @gcell_INCLUDES@
@@ -111,13 +111,13 @@ GCELL_SPU_INCLUDES = @gcell_spu_INCLUDES@
 GCELL_SPU_LA = @gcell_spu_LA@
 
 # libtool aware wrapper for ppu-embedspu
-GCELL_EMBEDSPU_LIBTOOL = @abs_top_srcdir@/gcell/lib/runtime/gcell-embedspu-libtool
+GCELL_EMBEDSPU_LIBTOOL = @top_srcdir@/gcell/lib/runtime/gcell-embedspu-libtool
 
 # Fix for BSD make not defining $(RM).  We define it now in configure.ac
 # using AM_PATH_PROG, but now here have to add a -f to be like GNU make
 RM=$(RM_PROG) -f
 
-RUN_GUILE = GUILE_LOAD_PATH="@abs_top_srcdir@/gruel/src/scheme" @GUILE@ -e main -s
+RUN_GUILE = GUILE_LOAD_PATH="@top_srcdir@/gruel/src/scheme" @GUILE@ -e main -s
 
 # Base directory for example applications
 exampledir = $(datadir)/gnuradio/examples
diff --git a/configure.ac b/configure.ac
index f923786..d55e4b2 100644
--- a/configure.ac
+++ b/configure.ac
@@ -62,6 +62,15 @@ AM_PATH_PYTHON
 AM_CONDITIONAL([PYTHON], [test x$enable_python = xyes])
 AM_CONDITIONAL([GUILE], [test x$enable_guile = xyes])
 
+AC_ARG_ENABLE(doxygen,
+	[AS_HELP_STRING(
+		[--disable-doxygen],
+		[Disable generation of documentation using doxygen],
+	)],
+	[doxygen=$enableval], [doxygen="yes"])
+AC_PATH_PROG(DOXYGEN,doxygen,false)
+AM_CONDITIONAL(HAVE_DOXYGEN, test $DOXYGEN != false && test "x$doxygen" = "xyes")
+
 AC_CHECK_PROG([XMLTO],[xmlto],[yes],[])
 AM_CONDITIONAL([HAS_XMLTO], [test x$XMLTO = xyes])
 
@@ -83,10 +92,6 @@ AC_CONFIG_FILES([
   host/apps/Makefile
   firmware/Makefile
   firmware/include/Makefile
-  firmware/lib/Makefile
-  firmware/src/Makefile
-  firmware/src/common/Makefile
-  firmware/src/usrp2/Makefile
   fpga/Makefile
   fpga/rbf/Makefile
   fpga/rbf/rev2/Makefile
diff --git a/doc/Makefile.am b/doc/Makefile.am
index 6abbe64..b8686dc 100644
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -27,6 +27,8 @@ SUBDIRS = other
 man3dir = $(mandir)/man3
 usrp_docdir  = $(prefix)/share/doc/usrp-$(DOCVER)
 
+if HAVE_DOXYGEN
+
 EXTRA_DIST += 			\
 	Doxyfile.in		\
 	ddc.eps			\
@@ -49,7 +51,7 @@ dist_usrp_doc_DATA = $(top_srcdir)/README
 dox: html/index.html
 html/index.html:
 	$(MKDIR_P) html
-	@DOXYGEN@
+	$(DOXYGEN) Doxyfile
 
 docbook-html: usrp_guide.html
 
@@ -65,7 +67,9 @@ install-data-local:
 	cp -r html $(DESTDIR)$(usrp_docdir)
 
 uninstall-local:
-	$(RM) -fr $(DESTDIR)$(usrp_docdir)/html
+	rm -rf $(DESTDIR)$(usrp_docdir)/html
 
 clean-local:
-	$(RM) -fr latex html man xml $(DOCBOOK_HTML_FILES)
+	rm -rf latex html man xml $(DOCBOOK_HTML_FILES)
+
+endif HAVE_DOXYGEN
diff --git a/firmware/Makefile.am b/firmware/Makefile.am
index 9c0da35..edef571 100644
--- a/firmware/Makefile.am
+++ b/firmware/Makefile.am
@@ -19,4 +19,5 @@
 # Boston, MA 02110-1301, USA.
 # 
 
-SUBDIRS = include lib src
+SUBDIRS = include
+# compilation broken: SUBDIR += lib src
diff --git a/host/lib/Makefile.am b/host/lib/Makefile.am
index a0de559..7311943 100644
--- a/host/lib/Makefile.am
+++ b/host/lib/Makefile.am
@@ -30,7 +30,7 @@ libusrp_la_common_LIBADD = 		\
 	$(USB_LIBS) 			\
 	$(BOOST_THREAD_LIB)		\
 	$(BOOST_SYSTEM_LIB)		\
-	../misc/libmisc.la
+	$(top_builddir)/host/misc/libmisc.la
 
 AM_CPPFLAGS = $(common_INCLUDES) $(BOOST_CPPFLAGS) $(WITH_INCLUDES)
 libusrp_la_LIBADD = $(libusrp_la_common_LIBADD)
@@ -40,7 +40,7 @@ EXTRA_DIST += 				\
 	std_paths.h.in			\
 	usrp_dbid.dat
 
-BUILT_SOURCES += $(abs_top_builddir)/usrp/host/include/usrp/usrp_dbid.h
+BUILT_SOURCES += $(top_builddir)/usrp/host/include/usrp/usrp_dbid.h
 
 BUILT_SOURCES += usrp_dbid.cc \
 		 usrp_dbid.py