Description: Debian build setup and shared libraries
 This patch turns all private FSL libraries into shared libs.
--- a/config/common/rules.mk
+++ b/config/common/rules.mk
@@ -32,7 +32,7 @@
 	${RM} -f /tmp/fslgrot *.o *.a *.exe core depend.mk
 
 install:
-	@${MAKE} "DESTDIR=${FSLDEVDIR}" master-install-script
+	@${MAKE} "DESTDIR=${DEB_DESTDIR}" master-install-script
 
 install-fmrib: 
 	@numunst=`cvs status | grep "Sticky Tag" | grep -v -i stable | wc -l` ; export numunst ; \
@@ -317,4 +317,4 @@
 		fi \
 	done
 
-include depend.mk
+#include depend.mk
--- a/config/common/vars.mk
+++ b/config/common/vars.mk
@@ -3,13 +3,15 @@
 INCDIR = ${FSLDIR}/include
 LIBDIR = ${FSLDIR}/lib
 
-DEVINCDIR = ${FSLDEVDIR}/include
-DEVLIBDIR = ${FSLDEVDIR}/lib
-
-DESTDIR = ${FSLDEVDIR}
-
-dest_INCDIR = ${DESTDIR}/include
-dest_LIBDIR = ${DESTDIR}/lib
+# for the Debian build FSLDIR and FSLDEVDIR is the same
+DEVINCDIR = ${FSLDIR}/include
+DEVLIBDIR = ${FSLDIR}/lib
+
+DESTDIR = ${DEB_DESTDIR}
+
+# do not install the libs and headers with the binaries
+dest_INCDIR = ${FSLDIR}/include
+dest_LIBDIR = ${FSLDIR}/lib
 dest_BINDIR = ${DESTDIR}/bin
 dest_MANDIR = ${DESTDIR}/man
 dest_TCLDIR = ${DESTDIR}/tcl
@@ -35,7 +37,8 @@
 	${AccumulatedIncFlags}
 
 HFILES = *.h
-AFILES = *.a
+# install the shared libs as well
+AFILES = *.a *.so
 XFILES = 
 SCRIPTS =
 TCLFILES = *.tcl
--- a/config/default.mk
+++ b/config/default.mk
@@ -1,6 +1,7 @@
 # Assumes that ${FSLDIR} is set as an environment variable
 
-include ${FSLCONFDIR}/${FSLMACHTYPE}/systemvars.mk
-include ${FSLCONFDIR}/${FSLMACHTYPE}/externallibs.mk
+# use Debian specific build configuration
+include ${FSLDIR}/debian/systemvars.mk
+include ${FSLDIR}/debian/externallibs.mk
 include ${FSLCONFDIR}/common/vars.mk
 include ${FSLCONFDIR}/common/rules.mk
--- a/extras/src/cprob/Makefile
+++ b/extras/src/cprob/Makefile
@@ -8,13 +8,12 @@
 
 USRCFLAGS = -std=gnu99
 
-all: libprob.a
+all: libprob
 
 dftest: all dftest.o
 	$(CC) $(CFLAGS) -L. -o dftest dftest.o -lprob
 
-libprob.a: $(OBJS) $(INCS)
-	ar rv libprob.a $(OBJS)
-	ranlib libprob.a
-	rm -f libcprob.a
-	ln -s libprob.a libcprob.a
+libprob: $(OBJS) $(INCS)
+	${CXX} -shared -o libprob.so $(OBJS) -fPIC ${LDFLAGS}
+	rm -f libcprob.so
+	ln -s libprob.so libcprob.so
--- a/src/fdt/Makefile
+++ b/src/fdt/Makefile
@@ -10,7 +10,7 @@
 USRINCFLAGS = -I${INC_NEWMAT} -I${INC_NEWRAN} -I${INC_CPROB} -I${INC_PROB} -I${INC_BOOST} -I${INC_ZLIB}
 USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_NEWRAN} -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_ZLIB}
 
-DLIBS = -lwarpfns -lbasisfield -lmeshclass -lnewimage -lutils -lmiscmaths -lnewmat -lnewran -lfslio -lniftiio -lznz -lcprob -lprob -lm -lz
+DLIBS = -lwarpfns -lbasisfield -lmeshclass -lbint -lnewimage -lutils -lmiscmaths -lnewmat -lfslio -lniftiio -lznz -lprob -lm -lz
 
 DTIFIT=dtifit
 CCOPS=ccops
@@ -155,7 +155,7 @@ ${EDDYCOMBINE}: ${EDDYCOMBINEOBJS}
 		   ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${EDDYCOMBINEOBJS} ${DLIBS}
 
 ${LIBBEDPOSTX_CUDA}: 
-		${CUDA}/bin/nvcc --shared --compiler-options '-fPIC' -o CUDA/libbedpostx_cuda.so CUDA/init_gpu.cu CUDA/samples.cu CUDA/diffmodels.cu CUDA/runmcmc.cu  CUDA/xfibres_gpu.cu -O3  -gencode=arch=compute_20,code=\"sm_20,compute_20\" -gencode=arch=compute_35,code=\"sm_35,compute_35\"  -lcudart -lcuda -lcurand -I. -L${CUDA}/lib64 -L${CUDA}/lib -ICUDA/options -I${CUDA}/include/thrust -I${FSLDIR}/extras/include/newmat -I${FSLDIR}/include -I${FSLDIR}/extras/include/boost -maxrregcount=64
+		${CUDA}/bin/nvcc --shared --compiler-options '-fPIC' -o CUDA/libbedpostx_cuda.so CUDA/init_gpu.cu CUDA/samples.cu CUDA/diffmodels.cu CUDA/runmcmc.cu  CUDA/xfibres_gpu.cu -O3  -gencode=arch=compute_20,code=\"sm_20,compute_20\" -gencode=arch=compute_35,code=\"sm_35,compute_35\"  -lcudart -lcuda -lcurand -I. -L${CUDA}/lib64 -L${CUDA}/lib -ICUDA/options -I${CUDA}/include/thrust -I${FSLDIR}/extras/include/newmat -I${FSLDIR}/include -I${FSLDIR}/extras/include/boost -maxrregcount=64 -DBOOST_NOINLINE='__attribute__ ((noinline))'
 		@if [ ! -d ${FSLDEVDIR}/lib/ ] ; then ${MKDIR} ${FSLDEVDIR}/lib ; fi
 		${CP} -rf CUDA/libbedpostx_cuda.so ${FSLDEVDIR}/lib
 
--- a/src/fslio/Makefile
+++ b/src/fslio/Makefile
@@ -8,10 +8,10 @@
 
 SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv
 
-all: libfslio.a
+all: libfslio
 
-libfslio.a: ${OBJS}
-	${AR} -r libfslio.a ${OBJS}
+libfslio: ${OBJS}
+	${CXX} -shared -o libfslio.so $(OBJS) -fPIC ${LDFLAGS} -lniftiio -lznz -lz
 
 TESTOBJS = exttest.o
 TESTLIBS = -lfslio -lniftiio -lznz -lz
--- a/src/fslio/fslio.h
+++ b/src/fslio/fslio.h
@@ -25,8 +25,8 @@
 #define __FSLIO_H
 
 #include <stdio.h>
-#include "niftiio/nifti1_io.h"
-#include "znzlib/znzlib.h"
+#include <nifti1_io.h>
+#include <znzlib.h>
 #include "dbh.h"
 
 #ifdef __cplusplus
--- a/src/libvis/Makefile
+++ b/src/libvis/Makefile
@@ -4,7 +4,7 @@
 
 PROJNAME = libvis
 
-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${INC_BOOST}
+USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${INC_BOOST} -fPIC
 USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
 
 LIBS = -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
@@ -21,10 +21,10 @@
 all: miscplot miscpic
 
 miscplot: ${PLOTOBJS}
-	${AR} -r libmiscplot.a ${PLOTOBJS}
+	${CXX} -shared -o libmiscplot.so ${PLOTOBJS} ${LDFLAGS} -lnewmat -lgd -lgdc -lmiscmaths -lfslio -lprob -lniftiio
 
 miscpic: ${PICOBJS}
-	${AR} -r libmiscpic.a ${PICOBJS}
+	${CXX} -shared -o libmiscpic.so ${PICOBJS} ${LDFLAGS} -lnewimage -lgd -lfslio -lmiscmaths -lnewmat -lniftiio
 
 test: ${TOBJS}
-	$(CXX) ${CXXFLAGS} ${LDFLAGS} -o $@ ${TOBJS} ${LIBS}
+	$(CXX) ${CXXFLAGS} ${LDFLAGS} -o $@ ${TOBJS}
--- a/src/melodic/Makefile
+++ b/src/melodic/Makefile
@@ -66,7 +66,7 @@
 all: ggmix fsl_regfilt fsl_glm melodic ${OTHERFILES}
 
 ggmix: ${GGMIX_OBJS}
-	${AR} -r libggmix.a ${GGMIX_OBJS} 
+	${CXX} -shared -o libggmix.so ${GGMIX_OBJS} ${LDFLAGS} -fPIC -lnewmat -lmiscmaths -lnewimage
 
 melodic: ${MELODIC_OBJS}
 	$(CXX) ${CXXFLAGS} ${LDFLAGS} -o $@ ${MELODIC_OBJS} ${LIBS}
--- a/src/meshclass/Makefile
+++ b/src/meshclass/Makefile
@@ -16,10 +16,10 @@
 
 DBGFLAGS=-g
 
-all: meshclass.a ${XFILES}
+all: meshclass ${XFILES}
 
-meshclass.a: ${MESHOBJS}
-	${AR} -r libmeshclass.a ${MESHOBJS}
+meshclass: ${MESHOBJS}
+	${CXX} -shared -o libmeshclass.so ${MESHOBJS} ${LDFLAGS} -fPIC
 
 drawmesh:${DRAWOBJS} 
 	${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${DRAWOBJS} ${LIBS} 
--- a/src/miscmaths/Makefile
+++ b/src/miscmaths/Makefile
@@ -14,10 +14,10 @@
 # The target "all" should ALWAYS be provided
 #   typically it will just be another target name
 
-all: libmiscmaths.a
+all: libmiscmaths
 
 quick:${OBJS} quick.o
 	${CXX}  ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} quick.o ${LIBS}
 
-libmiscmaths.a: ${OBJS}
-	${AR} -r libmiscmaths.a ${OBJS}
+libmiscmaths: ${OBJS}
+	${CXX} -shared -o libmiscmaths.so ${OBJS} -fPIC ${LDFLAGS} -lnewmat -lutils -lfslio -lniftiio -lprob
--- a/src/mm/Makefile
+++ b/src/mm/Makefile
@@ -13,10 +13,10 @@
 
 #OPTFLAGS =
 
-all:	${XFILES} libmm.a
+all:	${XFILES} libmm
 
-libmm.a: ${OBJS}
-	${AR} -r libmm.a ${OBJS}
+libmm: ${OBJS}
+	${CXX} -shared -o libmm.so ${OBJS} ${LDFLAGS} -fPIC -lmiscpic -lnewmat -lnewimage -lmiscmaths -lfslio -lutils -lprob -lmiscplot -lgd
 
 mm:${OBJS} mm.o
 	${CXX}  ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} mm.o ${LIBS}
--- a/src/newimage/Makefile
+++ b/src/newimage/Makefile
@@ -18,10 +18,10 @@
 TESTXFILES = testprog skeletonapp
 XFILES = 
 
-all: libnewimage.a
+all: libnewimage
 
-libnewimage.a: ${NOBJS}
-	${AR} -r libnewimage.a ${NOBJS}
+libnewimage: ${NOBJS}
+	${CXX} -shared -o libnewimage.so ${NOBJS} ${LDFLAGS} -fPIC -lnewmat -lfslio -lmiscmaths -lniftiio
 
 skeletonapp: ${SOBJS}
 	$(CXX)  ${CXXFLAGS} ${LDFLAGS} -o $@ ${SOBJS} ${LIBS}
--- a/src/newimage/newimage.h
+++ b/src/newimage/newimage.h
@@ -80,7 +80,7 @@
 #include "positerators.h"
 #include "miscmaths/miscmaths.h"
 #include "miscmaths/kernel.h"
-#include "niftiio/nifti1.h"
+#include <nifti1.h>
 #include "miscmaths/splinterpolator.h"
  
 using namespace NEWMAT;
--- a/src/shapeModel/Makefile
+++ b/src/shapeModel/Makefile
@@ -8,10 +8,10 @@
 USRLDFLAGS = -L${LIB_NEWMAT}  -L${LIB_ZLIB}
  
 
-all: shapeModel.a 
+all: shapeModel
 
-shapeModel.a: ${SHAPEOBJS}
-	${AR} -r libshapeModel.a ${SHAPEOBJS}
+shapeModel: ${SHAPEOBJS}
+	${CXX} -shared -o libshapeModel.so ${SHAPEOBJS} ${LDFLAGS} -fPIC -lmeshclass -lnewimage -lnewmat -lfirst_lib -lfslvtkio -lmiscmaths
 
 
 
--- a/src/utils/Makefile
+++ b/src/utils/Makefile
@@ -11,7 +11,7 @@
 OptionsTestObjects = opttst.o
 OptionsTestLibrarys = -lutils
 
-LibraryTarget = libutils.a
+LibraryTarget = libutils.so
 LibraryObjects = matches.o functions.o usage.o check.o parse.o log.o time_tracer.o
 
 all: ${LibraryTarget}
@@ -21,9 +21,7 @@
 		${OptionsTestLibrarys}
 
 ${LibraryTarget}: ${LibraryObjects}
-	${RM} -f ${LibraryTarget}
-	${AR} -r $@ ${LibraryObjects}
-	${RANLIB} ${LibraryTarget}
+	${CXX} -shared -o $@ ${LibraryObjects} ${LDFLAGS} -fPIC -lnewmat
 
 XFILES = 
 AFILES = ${LibraryTarget}
--- a/src/ptx2/Makefile
+++ b/src/ptx2/Makefile
@@ -16,7 +16,7 @@
 USRINCFLAGS = -I${INC_NEWMAT} -I${INC_NEWRAN} -I${INC_CPROB} -I${INC_PROB} -I${INC_BOOST} -I${INC_ZLIB}
 USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_NEWRAN} -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_ZLIB}
 
-DLIBS =  -lwarpfns -lbasisfield -lfslsurface  -lfslvtkio -lmeshclass -lnewimage -lutils -lmiscmaths -lnewmat -lnewran -lfslio -lgiftiio -lexpat -lfirst_lib -lniftiio -lznz -lcprob -lutils -lprob -lm -lz
+DLIBS = -lwarpfns -lbasisfield -lfslsurface  -lfslvtkio -lmeshclass -lnewimage -lutils -lmiscmaths -lnewmat -lfslio -lgiftiio -lexpat -lfirst_lib -lniftiio -lznz -lcprob -lutils -lprob -lm -lz
 
 
 CCOPS=ccops
--- a/src/qboot/Makefile
+++ b/src/qboot/Makefile
@@ -5,7 +5,7 @@
 USRINCFLAGS = -I${INC_NEWMAT} -I${INC_NEWRAN} -I${INC_CPROB} -I${INC_PROB} -I${INC_BOOST} -I${INC_ZLIB}
 USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_NEWRAN} -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_ZLIB}
 
-DLIBS = -lnewimage -lutils -lmiscmaths -lnewmat -lnewran -lfslio -lniftiio -lznz -lcprob -lprob -lm -lz
+DLIBS = -lnewimage -lutils -lmiscmaths -lnewmat -lfslio -lniftiio -lznz -lcprob -lprob -lm -lz
 
 QBOOT=qboot
 
@@ -19,4 +19,4 @@
 
 all: qboot
 ${QBOOT}:	   ${QBOOTOBJS}
-		   ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${QBOOTOBJS} ${DLIBS}
\ No newline at end of file
+		   ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${QBOOTOBJS} ${DLIBS}
--- a/src/fslsurface/fslsurfaceio.cc
+++ b/src/fslsurface/fslsurfaceio.cc
@@ -68,7 +68,7 @@
 #include <fslvtkio/fslvtkio.h>
 
 extern "C" {
-#include <giftiio/gifti_io.h>
+#include <gifti_io.h>
 }
 
 using namespace fslvtkio;
--- a/src/fslsurface/fslsurfaceio.h
+++ b/src/fslsurface/fslsurfaceio.h
@@ -71,7 +71,7 @@
 #include <vector>
 
 extern "C" {
-#include <giftiio/gifti_io.h>
+#include <gifti_io.h>
 }
 
 
--- a/src/fslvtkio/Makefile
+++ b/src/fslvtkio/Makefile
@@ -12,10 +12,10 @@
  
 MODELOBJS=fslvtkio.o
 
-all: fslvtkio.a 
+all: fslvtkio
 
-fslvtkio.a: ${SHAPEOBJS}
-	${AR} -r libfslvtkio.a ${SHAPEOBJS}
+fslvtkio: ${SHAPEOBJS}
+	${CXX} -shared -o libfslvtkio.so $(SHAPEOBJS) -fPIC ${LDFLAGS} ${LIBS}