diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..425a7ca
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,16 @@
+.deps/
+/aclocal.m4
+/autom4te.cache/
+/config.h.in
+/config.h
+/config.log
+/config.status
+/configure
+/config/test-driver
+/stamp-h1
+/HTML5-frontend/jquery-1.4.4.min.js
+*.stamp
+Makefile
+Makefile.in
+bin/
+dist/
\ No newline at end of file
diff --git a/Admin/Makefile.am b/Admin/Makefile.am
index deb15ad..7a10d55 100644
--- a/Admin/Makefile.am
+++ b/Admin/Makefile.am
@@ -19,6 +19,7 @@ GCJLINK = $(GCJLD)
 NDTGCJFLAGS = -d bin -sourcepath src
 CLASSPATH_ENV = 
 TEMPDIRS = bin
+AUTOMAKE_OPTIONS = no-exeext
 
 noinst_PROGRAMS	= Admin.class
 
diff --git a/Applet/Makefile.am b/Applet/Makefile.am
index ee28d87..e4dbbe3 100644
--- a/Applet/Makefile.am
+++ b/Applet/Makefile.am
@@ -21,6 +21,7 @@ jsonlib = lib/json-simple-1.1.1.jar
 NDTGCJFLAGS = -d bin -sourcepath src -cp $(jsonlib)
 NDTJARSIGNERFLAG = -keystore
 TEMPDIRS = bin dist
+AUTOMAKE_OPTIONS = no-exeext
 
 ndtdir = $(prefix)/ndt
 jsonlibdir = $(ndtdir)/lib
diff --git a/Makefile.am b/Makefile.am
index 502eae4..e3e0a83 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -16,6 +16,8 @@
 #	Description:	toplevel build for bwctl
 #
 
+ACLOCAL_AMFLAGS = -I config
+
 SUBDIRS = @TOP_BUILD_DIRS@ src conf doc HTML5-frontend
 
 if INCLUDE_APPLET
diff --git a/config/c-attribute.m4 b/config/c-attribute.m4
deleted file mode 100644
index d63f68f..0000000
--- a/config/c-attribute.m4
+++ /dev/null
@@ -1,30 +0,0 @@
-dnl
-dnl	$Id$
-dnl
-
-dnl
-dnl	This macro is used to test for the gcc __attribute__ keyword.
-dnl
-
-AC_DEFUN(I2_C___ATTRIBUTE__, [
-AC_MSG_CHECKING(for __attribute__)
-AC_CACHE_VAL(ac_cv___attribute__, [
-AC_TRY_COMPILE([
-#include <stdlib.h>
-],
-[
-static void foo(void) __attribute__ ((noreturn));
-
-static void
-foo(void)
-{
-  exit(1);
-}
-],
-ac_cv___attribute__=yes,
-ac_cv___attribute__=no)])
-if test "$ac_cv___attribute__" = "yes"; then
-  AC_DEFINE(HAVE___ATTRIBUTE__, 1, [define if your compiler has __attribute__])
-fi
-AC_MSG_RESULT($ac_cv___attribute__)
-])
diff --git a/configure.ac b/configure.ac
index 1932563..3452291 100644
--- a/configure.ac
+++ b/configure.ac
@@ -31,6 +31,7 @@
 # AC_PREREQ(2.57)
 AC_INIT([NDT],[4.0.0.1],[ndt-user@internet2.edu])
 AC_CONFIG_AUX_DIR(config)
+AC_CONFIG_MACRO_DIR(config)
 # AM_INIT_AUTOMAKE(NDT, v1.0, [no-define])
 AM_INIT_AUTOMAKE
 AC_CONFIG_SRCDIR([src/analyze.c])
@@ -222,9 +223,9 @@ OLD_LDFLAGS="$LDFLAGS"
 OLD_CFLAGS="$CFLAGS"
 
 CFLAGS="$CFLAGS $I2UTILINCS"
-LDFLAGS="$CFLAGS $I2UTILLDFLAGS"
+LDFLAGS="$LDFLAGS $I2UTILLDFLAGS"
 
-AC_SEARCH_LIBS([I2AddrByNode],I2util, HAVE_I2UTIL_LIBS=1,HAVE_I2UTIL_LIBS=0)
+AC_CHECK_LIB([I2util], [I2AddrByNode], HAVE_I2UTIL_LIBS=1, HAVE_I2UTIL_LIBS=0)
 AC_CHECK_HEADERS([I2util/util.h I2util/conf.h], HAVE_I2UTIL_HEADERS=1,HAVE_I2UTIL_HEADERS=0)
 
 LDFLAGS="$OLD_LDFLAGS"
@@ -233,9 +234,13 @@ CFLAGS="$OLD_CFLAGS"
 if test "$HAVE_I2UTIL_HEADERS" != "1" || test "$HAVE_I2UTIL_LIBS" != "1"; then
 	# now, check for sub-build/sub-configure
 	if test -d I2util/I2util; then
+		# clear the cache
+		AS_UNSET([ac_cv_lib_I2util_I2AddrByNode])
+		AS_UNSET([ac_cv_header_I2util_util_h])
+		AS_UNSET([ac_cv_header_I2util_conf_h])
 		AC_CONFIG_SUBDIRS(I2util)
 		TOP_BUILD_DIRS="I2util $TOP_BUILD_DIRS"
-		I2util_dir='${top_srcdir}/I2util'
+		I2util_dir="`pwd`/I2util"
 		I2UTILINCS="-I$I2util_dir $I2UTILINCS"
 		I2UTILLDFLAGS="-L$I2util_dir/I2util $I2UTILLDFLAGS"
 		I2UTILLIBDEPS="$I2util_dir/I2util/libI2util.a"
@@ -249,15 +254,13 @@ if test "$HAVE_I2UTIL_HEADERS" != "1" || test "$HAVE_I2UTIL_LIBS" != "1"; then
 	OLD_CFLAGS="$CFLAGS"
 
         CFLAGS="$CFLAGS $I2UTILINCS"
-        LDFLAGS="$CFLAGS $I2UTILLDFLAGS"
+        LDFLAGS="$LDFLAGS $I2UTILLDFLAGS"
 
-        AC_SEARCH_LIBS([I2AddrByNode],I2util, ,AC_MSG_ERROR([Couldn't find I2util library]))
+        AC_CHECK_LIB([I2util], [I2AddrByNode], [:], AC_MSG_ERROR([Couldn't find I2util library]))
         AC_CHECK_HEADERS([I2util/util.h I2util/conf.h], ,AC_MSG_ERROR([Couldn't find I2util header files]), [AC_INCLUDES_DEFAULT])
 
 	LDFLAGS="$OLD_LDFLAGS"
 	CFLAGS="$OLD_CFLAGS"
-
-	I2UTILLIBS="$I2UTILLDFLAGS -lI2util"
 fi
 
 I2UTILLIBS="$I2UTILLDFLAGS -lI2util"
@@ -422,6 +425,7 @@ AC_C_CONST
 AC_HEADER_TIME
 
 # Checks for library functions.
+m4_pattern_forbid([^AX_])
 AX_CHECK_OPENSSL(AM_CONDITIONAL(HAVE_SSL, true), AM_CONDITIONAL(HAVE_SSL, false))
 
 AC_FUNC_ERROR_AT_LINE
diff --git a/flash-client/Makefile.am b/flash-client/Makefile.am
index 99e9228..2b9a046 100644
--- a/flash-client/Makefile.am
+++ b/flash-client/Makefile.am
@@ -16,6 +16,7 @@
 
 NDTMXMLCFLAGS = -o dist/FlashClt.swf -load-config+=ndt-flash-config.xml
 TEMPDIRS = dist
+AUTOMAKE_OPTIONS = no-exeext
 
 ndtdir = $(prefix)/ndt
 
diff --git a/janalyze/Makefile.am b/janalyze/Makefile.am
index 02c2883..abb41c8 100644
--- a/janalyze/Makefile.am
+++ b/janalyze/Makefile.am
@@ -17,8 +17,9 @@
 GCJLINK = $(GCJLD)
 CLASSPATH_ENV =
 NDTGCJFLAGS = -cp external:src/edu/internet2/ndt -d bin -sourcepath src
-GCJFLAGS =
+AM_GCJFLAGS =
 TEMPDIRS = bin dist
+AUTOMAKE_OPTIONS = no-exeext
 
 ndtdir = $(prefix)/ndt
 
@@ -52,7 +53,7 @@ create-packageDirs:
 install-JAnalyzeJAVA: classJAnalyze.stamp create-packageDirs
 	@$(NORMAL_INSTALL)
 	test -z "$(JAnalyzedir)" || $(mkdir_p) "$(DESTDIR)$(JAnalyzedir)"	
-	@test -z "$(JAnalyze_JAVA/bin/edu/internet2/ndt)" || for p in *.class; do \
+	@test -z "$(JAnalyze_JAVA)/bin/edu/internet2/ndt" || for p in *.class; do \
 		echo " $(INSTALL_DATA) '$$p' '$(DESTDIR)$(JAnalyzedir)/edu/internet2/ndt/$$p'"; \
 		$(INSTALL_DATA) "$$p" "$(DESTDIR)$(JAnalyzedir)/edu/internet2/ndt/$$p"; \
 	done
diff --git a/src/Makefile.am b/src/Makefile.am
index ec8f960..2e4271f 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -15,7 +15,7 @@
 #
 #  Description:
 
-INCLUDES  = $(NDTINCDIR) $(I2UTILINCS)
+AM_CPPFLAGS  = $(NDTINCDIR) $(I2UTILINCS)
 AM_LDFLAGS  = $(NDTLDFLAGS)
 AM_LIBS    = $(I2UTILLIBS)
 AM_CFLAGS  = $(NDTCFLAGS)