diff --git a/Makefile.am b/Makefile.am
index 4fe2ed1..7f3a95f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4
 
 AUTOMAKE_OPTIONS = gnits
 
-SUBDIRS = plplot ajax nucleus emboss test doc jemboss
+if !ESYSTEMLIBS
+EXTRA_DIRS = plplot
+endif
+
+if GJEMBOSS
+JEMBOSS_DIR = jemboss
+endif
+
+SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
+DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR)
 
 # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
 
 # files with nonstandard names in this directory
-EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
+EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh
 
 # tar to pick up the other directories
 # then remove any CVS subdirectories
diff --git a/README.fixes b/README.fixes
new file mode 100644
index 0000000..3c56d79
--- /dev/null
+++ b/README.fixes
@@ -0,0 +1,9 @@
+The files in this directory are bugfix replacements for files in
+the EMBOSS-6.3.1 distribution. Just drop the replacement files in
+the location shown and redo the 'make install.'
+
+Fix 1. EMBOSS-6.3.1/configure
+       EMBOSS-6.3.1/m4/mysql.m4
+
+21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of
+             hpdf support prevented inclusion of MySQL support.
diff --git a/ajax/Makefile.am b/ajax/Makefile.am
index 4a44f6f..cf27ff8 100644
--- a/ajax/Makefile.am
+++ b/ajax/Makefile.am
@@ -1,6 +1,6 @@
 ## Process this file with automake to produce Makefile.in
 if !ESYSTEMLIBS
-EXTRA_DIRS = expat zlib
+EXTRA_DIRS = pcre expat zlib
 endif
 
-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am
index 02bcaa7..368ddfe 100644
--- a/ajax/acd/Makefile.am
+++ b/ajax/acd/Makefile.am
@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
 endif
 
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES =  \
 $(EXTRA_INCLUDES) \
 -I$(top_srcdir)/ajax/core \
 -I$(top_srcdir)/ajax/graphics \
@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF)
 endif
 
 libacd_la_LDFLAGS = $(LINKFLAGS)
+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la
diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am
index da57727..857ca5f 100644
--- a/ajax/ajaxdb/Makefile.am
+++ b/ajax/ajaxdb/Makefile.am
@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
 endif
 
 
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = \
 $(EXTRA_INCLUDES) \
 -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
 
@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF)
 endif
 
 libajaxdb_la_LDFLAGS = $(LINKFLAGS)
+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am
index af27cb0..8fa4a3a 100644
--- a/ajax/core/Makefile.am
+++ b/ajax/core/Makefile.am
@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre 
+else
+EXTRA_LIBS = -lexpat -lpcre
 endif
 
+EXTRA_DIST = ajax-pcre-config.h.in
+DISTCLEAN = ajax-pcre-config.h
 
 INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
 -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
+$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS)
 
 AJAXSRC = ajalign.c ajarr.c ajassert.c \
 ajbase.c ajcall.c ajcod.c \
@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \
 ajmath.h ajmatrices.h ajmem.h ajmess.h \
 ajnam.h ajnexus.h ajobo.h \
 ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
-ajrange.h ajreg.h ajreport.h ajresource.h \
+ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \
 ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \
 ajsort.h ajsql.h ajstr.h ajsys.h \
 ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF)
 endif
 
 libajax_la_LDFLAGS = $(LINKFLAGS)
+libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS)
diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in
new file mode 100644
index 0000000..b09e4e6
--- /dev/null
+++ b/ajax/core/ajax-pcre-config.h.in
@@ -0,0 +1 @@
+@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE
diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h
index 06793be..659f462 100644
--- a/ajax/core/ajreg.h
+++ b/ajax/core/ajreg.h
@@ -16,9 +16,14 @@ extern "C"
 #define ajreg_h
 
 #include "ajax.h"
+#include "ajax-pcre-config.h"
+#ifndef AJAX_USE_SYSTEM_PCRE
 #include "pcre_config.h"
 #include "pcre_internal.h"
 #include "pcreposix.h"
+#else
+#include <pcre.h>
+#endif
 
 #define AJREG_OVECSIZE 30
 
@@ -41,7 +46,11 @@ extern "C"
 ******************************************************************************/
 
 typedef struct AjSRegexp {
+#ifndef AJAX_USE_SYSTEM_PCRE
     real_pcre *pcre;
+#else
+    pcre *pcre;
+#endif
     pcre_extra *extra;
     int *ovector;
     const char* orig;
diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am
index ca33a84..87e51bd 100644
--- a/ajax/ensembl/Makefile.am
+++ b/ajax/ensembl/Makefile.am
@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre 
 endif
 
 
-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
+INCLUDES = $(EXTRA_INCLUDES) \
+-I$(top_srcdir)/ajax/core
 
 ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
 ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF)
 endif
 
 libensembl_la_LDFLAGS = $(LINKFLAGS)
+libensembl_la_LIBADD = ../core/libajax.la
diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am
index ab45afc..f61c605 100644
--- a/ajax/graphics/Makefile.am
+++ b/ajax/graphics/Makefile.am
@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot
 endif
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
+EXTRA_LIBS = $(PLPLOT_LIBS)
 endif
 
 
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = \
 $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
 
 AJAXGSRC = ajgraph.c ajhist.c
@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF)
 endif
 
 libajaxg_la_LDFLAGS = $(LINKFLAGS)
+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c
index 25e75e4..60f2743 100644
--- a/ajax/graphics/ajgraph.c
+++ b/ajax/graphics/ajgraph.c
@@ -34,10 +34,8 @@
 #include <float.h>
 #define AZ 28
 
-
 #include "plplotP.h"
 
-
 static void     GraphArray(ajuint numofpoints,
 			   float *x, float *y);
 static void     GraphArrayGaps(ajuint numofpoints,
@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size)
 ** @@
 ******************************************************************************/
 
+#define _GNU_SOURCE
+#include <stdio.h>
+
 static void GraphSetName(const AjPGraph thys,
 			 const AjPStr txt, const char *ext)
 {
     if(!thys->ready)
     {
+#ifdef USE_PLXSFNAM_SHIM
+        char *fullname;
+#endif
         ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
+#ifdef USE_PLXSFNAM_SHIM
+        fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
+        ajDebug("=g= plsfnam ('%S') instead\n", fullname);
+        plsfnam(fullname);
+        free(fullname);
+#else
         plxsfnam(ajStrGetPtr(txt), ext);
+#endif
         ajStrAssignS(&graphBasename, txt);
         ajStrAssignC(&graphExtension, ext);
         if(ajStrGetCharFirst(graphExtension) == '.')
diff --git a/configure.in b/configure.in
index ddb4f81..3f4fe5e 100644
--- a/configure.in
+++ b/configure.in
@@ -235,15 +235,6 @@ AC_PROG_INSTALL
 AC_PROG_LN_S
 AC_PROG_MAKE_SET
 
-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
-if test "${with_x}" != "no" ; then
-if test "`uname -a | grep Darwin`"; then
-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
-if test ${OSXX} '>' '10.4'; then
-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
-fi
-fi
-fi
 
 # Checks for header files.
 #as# AC_PATH_X
@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove)
 #as# 		select socket sqrt strchr strcspn strdup strerror strpbrk \
 #as# 		strrchr strspn strstr strtol])
 
-if test "${with_x}" != "no" ; then
-LF_EMBOSS_PATH_XLIB
-fi
 
 dnl Library checks
 AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket")
@@ -316,14 +304,16 @@ CHECK_PNGDRIVER
 CHECK_AUTH
 CHECK_AMD64
 
+AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes")
+
 AX_LIB_MYSQL
 AX_LIB_POSTGRESQL
 
 CFLAGS="$CFLAGS $MYSQL_CFLAGS"
 LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
 
-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
+LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
 
 
 dnl Check for 'ant' for packaging Jemboss and export result
@@ -443,13 +433,36 @@ fi
 
 dnl Test if --enable-systemlibs given
 have_systemlibs=no
+DEFINE_USE_SYSTEM_PCRE="#undef"
 AC_ARG_ENABLE(systemlibs,
    AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]))
+AC_MSG_CHECKING(for systemlib usage)
 if test "${enable_systemlibs}" = "yes" ; then
     have_systemlibs=yes
+    DEFINE_USE_SYSTEM_PCRE="#define"
+    PKG_CHECK_MODULES([PLPLOT], [plplotd])
+    PKG_CHECK_MODULES([ZLIB], [zlib])
+else
+    dnl X11 is only used by plplot
+    dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+    if test "${with_x}" != "no" ; then
+    if test "`uname -a | grep Darwin`"; then
+    OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+    if test ${OSXX} '>' '10.4'; then
+    CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
+    fi
+    fi
+    fi
+    if test "${with_x}" != "no" ; then
+    LF_EMBOSS_PATH_XLIB
+    fi
+     AC_MSG_NOTICE(USING bundled LIBS)
 fi          
 AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
 AC_SUBST(ESYSTEMLIBS)
+AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
+AC_SUBST(PLPLOT_CFLAGS)
+AC_SUBST(PLPLOT_LIBS)
 
 
 
@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS)
 
 dnl Test if purify exists and if --enable-purify given if so
 dnl set "-g"
-
 AC_MSG_CHECKING(for purify)
 dnl if(purify -version) < /dev/null > /dev/null 2>&1; then
    AC_ARG_ENABLE(purify,
@@ -683,6 +695,7 @@ CHECK_THREADS
 
 
 AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
+ajax/core/ajax-pcre-config.h
 ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
 ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
 ajax/acd/Makefile
diff --git a/emboss/Makefile.am b/emboss/Makefile.am
index 0820517..a0257b2 100644
--- a/emboss/Makefile.am
+++ b/emboss/Makefile.am
@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \
 yank
 
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
 endif
 
-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
+INCLUDES = -I$(top_srcdir)/nucleus \
 	$(EXTRA_INCLUDES) \
 	-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
-	-I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
+	-I$(top_srcdir)/ajax/acd
 
 
 aaindexextract_SOURCES = aaindexextract.c
@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c
 treetypedisplay_SOURCES = treetypedisplay.c
 
 if !ESYSTEMLIBS
-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
+EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la
 endif
 
 
@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
 	../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
 	../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
 	$(EXTRA_LDS) \
-	../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
 	$(XLIB)
 
 pkgdata_DATA = emboss.default.template
diff --git a/m4/mysql.m4 b/m4/mysql.m4
index fe413af..ebea25c 100644
--- a/m4/mysql.m4
+++ b/m4/mysql.m4
@@ -1,4 +1,6 @@
-##### http://autoconf-archive.cryp.to/ax_lib_mysql.html
+# ===========================================================================
+#       http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html
+# ===========================================================================
 #
 # SYNOPSIS
 #
@@ -6,19 +8,18 @@
 #
 # DESCRIPTION
 #
-#   This macro provides tests of availability of MySQL client library
-#   of particular version or newer.
+#   This macro provides tests of availability of MySQL client library of
+#   particular version or newer.
 #
-#   AX_LIB_MYSQL macro takes only one argument which is optional. If
-#   there is no required version passed, then macro does not run
-#   version test.
+#   AX_LIB_MYSQL macro takes only one argument which is optional. If there
+#   is no required version passed, then macro does not run version test.
 #
 #   The --with-mysql option takes one of three possible values:
 #
 #   no - do not check for MySQL client library
 #
-#   yes - do check for MySQL library in standard locations
-#   (mysql_config should be in the PATH)
+#   yes - do check for MySQL library in standard locations (mysql_config
+#   should be in the PATH)
 #
 #   path - complete path to mysql_config utility, use this option if
 #   mysql_config can't be found in the PATH
@@ -33,27 +34,23 @@
 #
 #     HAVE_MYSQL
 #
-# LAST MODIFICATION
+# LICENSE
 #
-#   2006-07-16
-#   2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers,
-#                  which prevents gdb from displaying stack traces.
-#                  Changed mysql_config --cflags to mysql_config --include
+#   Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net>
 #
-# COPYLEFT
-#
-#   Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net>
-#
-#   Copying and distribution of this file, with or without
-#   modification, are permitted in any medium without royalty provided
-#   the copyright notice and this notice are preserved.
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved. This file is offered as-is, without any
+#   warranty.
+
+#serial 12
 
 AC_DEFUN([AX_LIB_MYSQL],
 [
     AC_ARG_WITH([mysql],
-        [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
+        AS_HELP_STRING([--with-mysql=@<:@ARG@:>@],
             [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config]
-        )],
+        ),
         [
         if test "$withval" = "no"; then
             want_mysql="no"
@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL],
         ],
         [want_mysql="yes"]
     )
+    AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program])
 
     MYSQL_CFLAGS=""
     MYSQL_LDFLAGS=""
     MYSQL_VERSION=""
 
     dnl
-    dnl Check MySQL libraries (libpq)
+    dnl Check MySQL libraries
     dnl
 
     if test "$want_mysql" = "yes"; then
 
-        if test -z "$MYSQL_CONFIG" -o test; then
-            AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no])
+        if test -z "$MYSQL_CONFIG" ; then
+            AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no])
         fi
 
         if test "$MYSQL_CONFIG" != "no"; then
@@ -90,35 +88,8 @@ dnl         MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`"
 
             MYSQL_VERSION=`$MYSQL_CONFIG --version`
 
-dnl It isn't enough to just test for mysql_config as Fedora
-dnl provides it in the mysql RPM even though mysql-devel may
-dnl not be installed
-
-    	    EMBCFLAGS=$CFLAGS
-	    EMBLDFLAGS=$LDFLAGS
-	    CFLAGS=$MYSQL_CFLAGS
-	    LDFLAGS=$MYSQL_LDFLAGS
-
-            AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
-                                              #include "mysql.h"]],
-					    [[mysql_info(NULL)]])],
-			   [havemysql=yes],
-			   [havemysql=no])
-
-	    CFLAGS=$EMBCFLAGS
-	    LDFLAGS=$EMBLDFLAGS
-
-            if test "$havemysql" = yes; then
-                AC_DEFINE([HAVE_MYSQL], [1],
-                    [Define to 1 if MySQL libraries are available])
-                found_mysql="yes"
-                AC_MSG_RESULT([yes])
-            else
-	        MYSQL_CFLAGS=""
-	        MYSQL_LDFLAGS=""
-                found_mysql="no"
-                AC_MSG_RESULT([no])
-            fi
+            found_mysql="yes"
+            AC_MSG_RESULT([yes])
         else
             found_mysql="no"
             AC_MSG_RESULT([no])
@@ -170,6 +141,11 @@ dnl not be installed
         fi
     fi
 
+    if test "$found_mysql" = "yes" ; then
+        AC_DEFINE([HAVE_MYSQL], [1],
+                  [Define to 1 if MySQL libraries are available])
+    fi
+
     AC_SUBST([MYSQL_VERSION])
     AC_SUBST([MYSQL_CFLAGS])
     AC_SUBST([MYSQL_LDFLAGS])
diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am
index c244786..ff301b9 100644
--- a/nucleus/Makefile.am
+++ b/nucleus/Makefile.am
@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \
 -lezlib -leplplot
 else
 if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
 endif
 endif
 
 
-INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \
-	-I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
+INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
+	-I$(top_srcdir)/ajax \
 	$(EXTRA_INCLUDES) \
 	-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
@@ -55,3 +58,4 @@ LINKFLAGS =  $(VERS_INF)
 endif
 
 libnucleus_la_LDFLAGS =  $(LINKFLAGS)
+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la