diff --git a/.gitattributes b/.gitattributes
index b115b7f..5360024 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -526,6 +526,7 @@ src/include/H5_attribs.h -text
 src/include/H5_model.h -text
 src/include/H5hut.h -text
 src/include/Makefile.am -text
+src/include/h5core/Makefile.am -text
 src/include/h5core/h5.h -text
 src/include/h5core/h5_attribs.h -text
 src/include/h5core/h5_debug.h -text
diff --git a/Makefile.am b/Makefile.am
index 48b1381..2169895 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,9 +1,11 @@
 ACLOCAL_AMFLAGS = -I m4
+EXTRA_DIST = autogen.sh
 
-SUBDIRS = \
-	src \
-	test \
-	tools
+SUBDIRS =	\
+	src	\
+	test	\
+	tools	\
+	doc
 
 MAINTAINERCLEANFILES = \
 	config.h \
diff --git a/configure.ac b/configure.ac
index 1d8ecf1..f7f38f6 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([H5hut], [1.99.10], [h5part@lists.psi.ch], H5hut)
+AC_INIT([H5hut], [1.99-trunk], [h5part@lists.psi.ch], H5hut)
 AC_PREREQ(2.60)
 AC_CONFIG_HEADERS(config.h)
 AC_CONFIG_MACRO_DIR([m4])
@@ -117,8 +117,6 @@ PATH_Search() {
 ###############################################################################
 # MISC SETTINGS INCLUDING C & C++ COMPILER SETTING
 
-# Compute the canonical host-system type variable, host, and its three
-# individual parts host_cpu, host_vendor, and host_os.
 AC_CANONICAL_HOST
 AC_PROG_MAKE_SET
 
@@ -134,8 +132,6 @@ else
 fi
 
 # Determine a C/C++ compiler to use. 
-# If CC is not already set in the environment, check for other C compilers. 
-# Set output variable CC to the name of the compiler found.
 if test "x$ENABLE_PARALLEL" = "xyes"; then
    	CCOMPILERS="mpicc"
 	CXXCOMPILERS="mpic++"
@@ -149,17 +145,12 @@ CC=`which $CC`
 AC_PROG_CXX($CXXCOMPILERS)
 CXX=`which $CXX`
 
-# Use macro to set C99 mode instead of checking for gcc, which breaks with
-# parallel builds.
 AC_PROG_CC_C99
 if test "x$ac_cv_prog_cc_c99" = "xno"; then
 	AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
 	exit 1
 fi
 
-# Set output variable INSTALL to the path of a BSD-compatible install program,
-# if one is found in the current PATH. 
-# Otherwise, set INSTALL to `dir/install-sh -c`
 AC_PROG_INSTALL
 AC_PROG_AWK
 
@@ -208,7 +199,6 @@ AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
 AC_MSG_CHECKING([if C interface enabled])
 if test "X$ENABLE_C" = "Xyes"; then
 	AC_MSG_RESULT([yes])
-	BINDINGS="$BINDINGS C"
 else
         AC_MSG_RESULT([no])
 fi
@@ -217,8 +207,6 @@ fi
 AC_MSG_CHECKING([if fortran interface enabled])
 if test "X$ENABLE_FORTRAN" = "Xyes"; then
 	AC_MSG_RESULT([yes])
-	BINDINGS="$BINDINGS Fortran"
-	LIB_FORTRAN="libH5hutF.la"
 
 	if test "X$ENABLE_PARALLEL" = "Xyes"; then
 		AC_PROG_FC(mpif90 mpif77)
@@ -246,7 +234,6 @@ if test "X$ENABLE_FORTRAN" = "Xyes"; then
 	`cd src/Fortran && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
 
 	if test -f src/Fortran/TestUnderscore ; then
-		UNDERSCORE_H=Underscore.h
 		`cd src/Fortran && ./TestUnderscore > Underscore.h`
 		AC_MSG_RESULT([ok])
 	else
@@ -350,21 +337,17 @@ fi
 ###############################################################################
 # EXPORTING VARIABLES & CREATING OUTPUT FILES
 AC_SUBST(HDF5_PREFIX)
-AC_SUBST(LUSTREROOT)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)
 AC_SUBST(AM_CPPFLAGS)
 AC_SUBST(AM_LDFLAGS)
-AC_SUBST(LIBS)
-AC_SUBST(UNDERSCORE_H)
-AC_SUBST(LIB_FORTRAN)
-AC_SUBST(BINDINGS)
 
 AC_CONFIG_FILES([
 	Makefile
 	src/Makefile
 	src/h5core/Makefile
 	src/include/Makefile
+	src/include/h5core/Makefile
         src/C/Makefile
         src/Fortran/Makefile
 	test/Makefile
diff --git a/src/include/h5core/Makefile.am b/src/include/h5core/Makefile.am
new file mode 100644
index 0000000..e1eb337
--- /dev/null
+++ b/src/include/h5core/Makefile.am
@@ -0,0 +1,24 @@
+otherincludedir = $(includedir)/h5core
+
+include_HEADERS =		\
+	h5.h			\
+	h5_attribs.h		\
+	h5_debug.h		\
+	h5_errorhandling.h	\
+	h5_model.h		\
+	h5_syscall.h		\
+	h5_types.h		\
+	h5b_attribs.h		\
+	h5b_model.h		\
+	h5b_io.h		\
+	h5t_adjacencies.h	\
+	h5t_map.h		\
+	h5t_model.h		\
+	h5t_retrieve.h		\
+	h5t_store.h		\
+	h5t_tags.h		\
+	h5u_model.h		\
+	h5u_io.h
+
+clean-local:
+	$(RM) *~
diff --git a/test/Makefile.am b/test/Makefile.am
index 0c56f1e..72d5936 100644
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -1,4 +1,4 @@
-AM_CPPFLAGS = -I$(top_srcdir)/src/include @AM_CPPFLAGS@
+AM_CPPFLAGS += -I$(top_srcdir)/src/include
 AM_LDFLAGS += -L${abs_top_builddir}/src/lib
 
 LDADD =
@@ -34,5 +34,4 @@ h5_attach_test_SOURCES = \
 		h5_attach_test.c
 
 clean-local:
-	${RM} -f *.h5
-
+	${RM} -f *.h5 *~
diff --git a/tools/vtk2h5grid/Makefile.am b/tools/vtk2h5grid/Makefile.am
index 1916ba9..bc67daa 100644
--- a/tools/vtk2h5grid/Makefile.am
+++ b/tools/vtk2h5grid/Makefile.am
@@ -2,12 +2,9 @@ AM_CPPFLAGS += -I${abs_top_builddir}/src/include -Wno-deprecated
 FFLAGS += -cpp $(AM_CPPFLAGS)
 AM_LDFLAGS += -L${abs_top_builddir}/src/lib
 
-LDADD = 
-LDADD += -lH5hut -lvtkCommon -lvtkIO
+LDADD = -lH5hut -lvtkIO -lvtkFiltering -lvtkCommon -lvtksys
 
-
-bin_PROGRAMS = 
-bin_PROGRAMS += vtk2h5grid
+bin_PROGRAMS = vtk2h5grid
 vtk2h5grid_SOURCES = vtk2h5grid.cc
 
 distclean-local: