Index: /trunk/psLib/configure.ac
===================================================================
--- /trunk/psLib/configure.ac	(revision 4980)
+++ /trunk/psLib/configure.ac	(revision 4981)
@@ -22,5 +22,5 @@
 SUBDIR="etc src test" dnl don't include 'swig', as it is optional
 
-SRCPATH="`pwd`/src"
+SRCPATH='$(top_srcdir)/src'
 SRCDIRS="sys astro db fft fits imageops math mathtypes types xml"
 SRCINC=`echo "${SRCDIRS=}" | ${SED} "s|\(\\w\+\)|-I\${SRCPATH=}/\1|g"`
@@ -28,5 +28,4 @@
 SRCSUBLIBS=`echo "${SRCDIRS=}" | ${SED} "s|\(\\w\+\)|\1/libpslib\1.la|g"`
 AC_SUBST(SRCSUBLIBS,${SRCSUBLIBS=})
-CFLAGS="${CFLAGS=} -I${SRCPATH=} ${SRCINC=}"
 AC_SUBST(SRCINC,${SRCINC=})
 
@@ -61,7 +60,4 @@
 AC_PREFIX_DEFAULT([`pwd`])
 test "$prefix" = NONE && prefix=`pwd`
-
-dnl Setup the info for psLib for pkg-config
-PSLIB_CFLAGS="-I${includedir}"
 
 dnl check for standard language functionality
@@ -111,14 +107,17 @@
 
   AC_MSG_CHECKING([MySQL cflags])
-  MYSQL_CFLAGS="`${MYSQL_CONFIG} --cflags`"
+  MYSQL_CFLAGS="`${MYSQL_CONFIG} --include`"
+  PSLIB_CFLAGS="${PSLIB_CFLAGS=} ${MYSQL_CFLAGS}"
   AC_MSG_RESULT([${MYSQL_CFLAGS}])
-  CFLAGS="${CFLAGS=} ${MYSQL_CFLAGS}"
 
   AC_MSG_CHECKING([MySQL link options])
-  MYSQL_LDFLAGS="`${MYSQL_CONFIG} --libs`"
-  AC_MSG_RESULT([${MYSQL_LDFLAGS}])
-  PSLIB_LIBS="${PSLIB_LIBS=} ${MYSQL_LDFLAGS}"
+  MYSQL_LIBS="`${MYSQL_CONFIG} --libs`"
+  PSLIB_LIBS="${PSLIB_LIBS=} ${MYSQL_LIBS}"
+  AC_MSG_RESULT([${MYSQL_LIBS}])
   AC_SUBST(TST_PSDB,"tst_psDB") dnl enable the test for psDB
 
+dnl AC_RUN_IFELSE() uses CFLAGS to find mysql_version.h
+  TMP_CFLAGS=${CFLAGS}
+  CFLAGS=${MYSQL_CFLAGS}
   AC_RUN_IFELSE([AC_LANG_PROGRAM(
 [[#include <stdlib.h>
@@ -132,10 +131,13 @@
     }
 ]])], [], [AC_MSG_ERROR([MySQL 4.1.2 or newer is required.  Obtain it at  http://www.mysql.com or use --with-mysql to specify location.])])
-
+  CFLAGS=${TMP_CFLAGS}
 else
+  dnl FIXME
   CFLAGS="${CFLAGS=} -DOMIT_PSDB"
   PSLIB_CFLAGS="${PSLIB_CFLAGS=} -DOMIT_PSDB"
   AC_MSG_RESULT([disable building MySQL functionality])
 fi
+
+AC_SUBST([MYSQL_CFLAGS])
 
 dnl ----------------- CFITSIO options --------------------
@@ -150,9 +152,10 @@
 [AS_HELP_STRING(--with-cfitsio-lib=DIR,Specify CFITSIO library directory.)],
 [CFITSIO_LDFLAGS="-L$withval"])
-CFLAGS="${CFLAGS=} $CFITSIO_CFLAGS"
-dnl LDFLAGS="${LDFLAGS} $CFITSIO_LDFLAGS -lcfitsio"
+PSLIB_CFLAGS="${PSLIB_CFLAGS=} ${CFITSIO_CFLAGS}"
 PSLIB_LIBS="${PSLIB_LIBS=} $CFITSIO_LDFLAGS -lcfitsio"
 AC_CHECK_HEADERS([fitsio.h],[],
    [AC_MSG_ERROR([CFITSIO is required.  Obtain it at  http://heasarc.gsfc.nasa.gov/docs/software/fitsio or use --with-cfitsio to specify location.])])
+
+AC_SUBST([CFITSIO_CFLAGS])
 
 dnl ------------------ FFTW3 options ---------------------
@@ -167,10 +170,11 @@
 [AS_HELP_STRING(--with-fftw3-lib=DIR,Specify FFTW version 3 library directory.)],
 [FFTW3_LDFLAGS="-L$withval"])
-CFLAGS="${CFLAGS=} $FFTW3_CFLAGS"
-dnl LDFLAGS="${LDFLAGS=} $FFTW3_LDFLAGS -lfftw3f"
+PSLIB_CFLAGS="${PSLIB_CFLAGS=} ${FFTW3_CFLAGS}"
 PSLIB_LIBS="${PSLIB_LIBS=} $FFTW3_LDFLAGS -lfftw3f"
 AC_MSG_CHECKING([FFTW header files])
 AC_CHECK_HEADERS([fftw3.h],[],
    [AC_MSG_ERROR([FFTW version 3 with float support is required.  Obtain it at http://www.fftw.org/or use --with-fftw3 to specify location.])])
+
+AC_SUBST([FFTW3_CFLAGS])
 
 dnl -------------------- GSL options ---------------------
@@ -184,7 +188,8 @@
 GSL_CFLAGS="`${GSL_CONFIG} --cflags`"
 AC_MSG_RESULT([${GSL_CFLAGS}])
-CFLAGS="${CFLAGS=} ${GSL_CFLAGS}"
-dnl LDFLAGS="${LDFLAGS=} `${GSL_CONFIG} --libs`"
+PSLIB_CFLAGS="${PSLIB_CFLAGS=} ${GSL_CFLAGS}"
 PSLIB_LIBS="${PSLIB_LIBS=} `${GSL_CONFIG} --libs`"
+
+AC_SUBST([GSL_CFLAGS])
 
 dnl ------------------- XML2 options ---------------------
@@ -198,9 +203,8 @@
 XML_CFLAGS="`${XML_CONFIG} --cflags`"
 AC_MSG_RESULT([${XML_CFLAGS}])
-CFLAGS="${CFLAGS=} ${XML_CFLAGS}"
-dnl LDFLAGS="${LDFLAGS=} `${XML_CONFIG} --libs`"
+PSLIB_CFLAGS="${PSLIB_CFLAGS=} ${XML_CFLAGS}"
 PSLIB_LIBS="${PSLIB_LIBS=} `${XML_CONFIG} --libs`"
-PSLIB_CFLAGS="${PSLIB_CFLAGS=} `${XML_CONFIG} --cflags`"
-
+
+AC_SUBST([XML_CFLAGS])
 
 dnl ------------------- SWIG options ---------------------
Index: /trunk/psLib/pslib-config.in
===================================================================
--- /trunk/psLib/pslib-config.in	(revision 4980)
+++ /trunk/psLib/pslib-config.in	(revision 4981)
@@ -57,5 +57,5 @@
 
     --cflags)
-       	echo @PSLIB_CFLAGS@
+       	echo -I@includedir@ @PSLIB_CFLAGS@
        	;;
 
Index: /trunk/psLib/pslib.pc.in
===================================================================
--- /trunk/psLib/pslib.pc.in	(revision 4980)
+++ /trunk/psLib/pslib.pc.in	(revision 4981)
@@ -8,3 +8,3 @@
 Version: @VERSION@
 Libs: -L@libdir@ -lpslib @PSLIB_LIBS@ @LIBS@
-Cflags: @PSLIB_CFLAGS@
+Cflags: -I${includedir} @PSLIB_CFLAGS@
Index: /trunk/psLib/src/Makefile.am
===================================================================
--- /trunk/psLib/src/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 lib_LTLIBRARIES = libpslib.la
 
+libpslib_la_CPPFLAGS = $(SRCINC)
 libpslib_la_LIBADD = $(SRCSUBLIBS)
 
Index: /trunk/psLib/src/astro/Makefile.am
===================================================================
--- /trunk/psLib/src/astro/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/astro/Makefile.am	(revision 4981)
@@ -4,4 +4,6 @@
 
 noinst_LTLIBRARIES = libpslibastro.la
+
+libpslibastro_la_CPPFLAGS = $(SRCINC)
 libpslibastro_la_SOURCES = \
 	psTime.c \
Index: /trunk/psLib/src/db/Makefile.am
===================================================================
--- /trunk/psLib/src/db/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/db/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibdb.la
 
+libpslibdb_la_CPPFLAGS = $(SRCINC) $(MYSQL_CFLAGS)
 libpslibdb_la_SOURCES = \
 	psDB.c
Index: /trunk/psLib/src/fft/Makefile.am
===================================================================
--- /trunk/psLib/src/fft/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/fft/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibfft.la
 
+libpslibfft_la_CPPFLAGS = $(SRCINC) $(FFTW3_CFLAGS)
 libpslibfft_la_SOURCES = \
 	psImageFFT.c \
Index: /trunk/psLib/src/fits/Makefile.am
===================================================================
--- /trunk/psLib/src/fits/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/fits/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibfits.la
 
+libpslibfits_la_CPPFLAGS = $(SRCINC) $(CFITSIO_CFLAGS) 
 libpslibfits_la_SOURCES = \
 	psFits.c
Index: /trunk/psLib/src/imageops/Makefile.am
===================================================================
--- /trunk/psLib/src/imageops/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/imageops/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibimageops.la
 
+libpslibimageops_la_CPPFLAGS = $(SRCINC)
 libpslibimageops_la_SOURCES = \
 	psImageConvolve.c \
Index: /trunk/psLib/src/math/Makefile.am
===================================================================
--- /trunk/psLib/src/math/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/math/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibmath.la
 
+libpslibmath_la_CPPFLAGS = $(SRCINC) $(GSL_CFLAGS)
 libpslibmath_la_SOURCES = \
 	psBinaryOp.c \
Index: /trunk/psLib/src/mathtypes/Makefile.am
===================================================================
--- /trunk/psLib/src/mathtypes/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/mathtypes/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibmathtypes.la
 
+libpslibmathtypes_la_CPPFLAGS = $(SRCINC)
 libpslibmathtypes_la_SOURCES = \
 	psImage.c \
Index: /trunk/psLib/src/sys/Makefile.am
===================================================================
--- /trunk/psLib/src/sys/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/sys/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibsys.la
 
+libpslibsys_la_CPPFLAGS = $(SRCINC)
 libpslibsys_la_SOURCES = \
 	psAbort.c \
Index: /trunk/psLib/src/types/Makefile.am
===================================================================
--- /trunk/psLib/src/types/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/types/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibtypes.la
 
+libpslibtypes_la_CPPFLAGS = $(SRCINC)
 libpslibtypes_la_SOURCES = \
 	psArray.c \
Index: /trunk/psLib/src/xml/Makefile.am
===================================================================
--- /trunk/psLib/src/xml/Makefile.am	(revision 4980)
+++ /trunk/psLib/src/xml/Makefile.am	(revision 4981)
@@ -3,4 +3,5 @@
 noinst_LTLIBRARIES = libpslibxml.la
 
+libpslibxml_la_CPPFLAGS = $(SRCINC) $(XML_CFLAGS)
 libpslibxml_la_SOURCES = \
 	psXML.c
Index: /trunk/psLib/swig/Makefile.am
===================================================================
--- /trunk/psLib/swig/Makefile.am	(revision 4980)
+++ /trunk/psLib/swig/Makefile.am	(revision 4981)
@@ -5,5 +5,7 @@
 	rm -rf psLibModule
 
-SRCDIR = $(shell cd $(top_srcdir) && pwd)
+# this is going into a make file one directory deeper in the tree so the
+# realitive paths need to be adjusted
+SWIGINC=`echo "${SRCINC}" | ${SED} "s|-I|-I../|g"`
 
 ####################################################
@@ -18,5 +20,5 @@
 psLibModule/setup.txt:
 	if [ ! -d psLibModule ]; then mkdir psLibModule; fi
-	echo "includes=$(SRCINC)" > psLibModule/setup.txt
+	echo "includes=-I../$(top_srcdir)/src $(SWIGINC) $(PSLIB_CFLAGS)" > psLibModule/setup.txt
 	echo "ldflags=-L$(top_builddir)/src $(PSLIB_LIBS)" >> psLibModule/setup.txt
 	echo "cflags=$(CFLAGS) -std=c99 -Wno-unused -Wno-strict-aliasing" >> psLibModule/setup.txt
Index: /trunk/psLib/test/astro/Makefile.am
===================================================================
--- /trunk/psLib/test/astro/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/astro/Makefile.am	(revision 4981)
@@ -2,4 +2,5 @@
 #
 
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 
Index: /trunk/psLib/test/db/Makefile.am
===================================================================
--- /trunk/psLib/test/db/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/db/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for db tests of psLib
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 
Index: /trunk/psLib/test/fft/Makefile.am
===================================================================
--- /trunk/psLib/test/fft/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/fft/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for fft tests of psLib
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 
Index: /trunk/psLib/test/fits/Makefile.am
===================================================================
--- /trunk/psLib/test/fits/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/fits/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for fits tests of psLib
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 
Index: /trunk/psLib/test/imageops/Makefile.am
===================================================================
--- /trunk/psLib/test/imageops/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/imageops/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for imageops tests of psLib
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 
Index: /trunk/psLib/test/math/Makefile.am
===================================================================
--- /trunk/psLib/test/math/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/math/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for math tests of psLib
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 
Index: /trunk/psLib/test/mathtypes/Makefile.am
===================================================================
--- /trunk/psLib/test/mathtypes/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/mathtypes/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for mathtypes tests
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 
Index: /trunk/psLib/test/sys/Makefile.am
===================================================================
--- /trunk/psLib/test/sys/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/sys/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for sys tests
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 
Index: /trunk/psLib/test/types/Makefile.am
===================================================================
--- /trunk/psLib/test/types/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/types/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for types tests
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)
 AM_CFLAGS = -DXML_CONFIG_FILE="\"$(top_srcdir)/etc/pslib/psTime.xml\""
Index: /trunk/psLib/test/xml/Makefile.am
===================================================================
--- /trunk/psLib/test/xml/Makefile.am	(revision 4980)
+++ /trunk/psLib/test/xml/Makefile.am	(revision 4981)
@@ -1,4 +1,5 @@
 #Makefile for types tests
 #
+AM_CPPFLAGS = $(SRCINC) $(PSLIB_CFLAGS)
 AM_LDFLAGS = -L$(top_builddir)/src -lpslib $(PSLIB_LIBS)