Use non-recursive make, as far as possible

17 files changed, 1207 insertions, 2092 deletions

diff --git a/.gitignore b/.gitignore
index 4984dfa5..2abcd80b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,4 +20,5 @@ src/cubeit
 src/reintegrate
 src/estimate_background
 src/check_hkl
+src/.dirstamp
 *~
diff --git a/Makefile.am b/Makefile.am
index 7e6224bd..43367dac 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,3 +1,152 @@
 EXTRA_DIST = configure m4/gnulib-cache.m4
-SUBDIRS = lib src data doc doc/examples scripts
+SUBDIRS = lib
 ACLOCAL_AMFLAGS = -I m4
+
+bin_PROGRAMS = src/pattern_sim src/process_hkl src/get_hkl src/indexamajig \
+               src/compare_hkl src/powder_plot src/render_hkl \
+               src/calibrate_detector src/facetron src/reintegrate \
+               src/estimate_background src/check_hkl
+
+if HAVE_GTK
+bin_PROGRAMS += src/hdfsee
+endif
+
+if HAVE_CAIRO
+bin_PROGRAMS += src/cubeit
+endif
+
+AM_CFLAGS = -Wall
+AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -I$(top_srcdir)/lib
+LDADD = $(top_builddir)/lib/libgnu.a
+
+src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c src/utils.c \
+                      src/image.c src/cell.c src/hdf5-file.c src/detector.c \
+                      src/sfac.c src/peaks.c src/reflections.c \
+                      src/beam-parameters.c src/symmetry.c
+if HAVE_OPENCL
+src_pattern_sim_SOURCES += src/diffraction-gpu.c src/cl-utils.c
+endif
+
+src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c src/cell.c \
+                      src/utils.c src/reflections.c src/symmetry.c \
+                      src/stream.c src/beam-parameters.c
+
+src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c src/utils.c src/cell.c \
+                      src/image.c src/peaks.c src/index.c src/filters.c \
+                      src/diffraction.c src/detector.c src/sfac.c src/dirax.c \
+                      src/mosflm.c src/reflections.c src/templates.c \
+                      src/symmetry.c src/geometry.c src/thread-pool.c \
+                      src/beam-parameters.c
+if HAVE_OPENCL
+src_indexamajig_SOURCES += src/diffraction-gpu.c src/cl-utils.c
+endif
+
+
+if HAVE_GTK
+src_hdfsee_SOURCES = src/hdfsee.c src/displaywindow.c src/render.c src/hdf5-file.c \
+                 src/utils.c src/image.c src/filters.c
+endif
+
+src_get_hkl_SOURCES = src/get_hkl.c src/sfac.c src/cell.c src/utils.c \
+                  src/reflections.c src/symmetry.c src/beam-parameters.c
+
+src_compare_hkl_SOURCES = src/compare_hkl.c src/sfac.c src/cell.c src/utils.c \
+                      src/reflections.c src/statistics.c src/symmetry.c
+
+src_check_hkl_SOURCES = src/check_hkl.c src/sfac.c src/cell.c src/utils.c \
+                    src/reflections.c src/statistics.c src/symmetry.c
+
+src_powder_plot_SOURCES = src/powder_plot.c src/cell.c src/utils.c src/image.c \
+                      src/hdf5-file.c src/detector.c
+
+src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflections.c src/utils.c \
+                     src/povray.c src/symmetry.c src/render.c src/hdf5-file.c \
+                     src/image.c src/filters.c
+
+src_calibrate_detector_SOURCES = src/calibrate_detector.c src/utils.c \
+                             src/hdf5-file.c src/image.c src/filters.c \
+                             src/peaks.c src/detector.c src/cell.c \
+                             src/thread-pool.c
+
+src_facetron_SOURCES = src/facetron.c src/cell.c src/hdf5-file.c src/utils.c \
+                   src/detector.c src/peaks.c src/image.c src/geometry.c \
+                   src/reflections.c src/stream.c src/thread-pool.c \
+                   src/beam-parameters.c src/symmetry.c src/post-refinement.c \
+                   src/hrs-scaling.c
+
+if HAVE_CAIRO
+src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
+                 src/detector.c src/render.c src/filters.c src/image.c \
+                 src/symmetry.c src/stream.c src/thread-pool.c
+endif
+
+src_reintegrate_SOURCES = src/reintegrate.c src/cell.c src/hdf5-file.c src/utils.c \
+                      src/detector.c src/peaks.c src/image.c src/stream.c \
+                      src/index.c src/dirax.c src/mosflm.c src/templates.c \
+                      src/geometry.c src/symmetry.c src/thread-pool.c
+
+src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
+                              src/utils.c src/cell.c
+
+INCLUDES = "-I$(top_srcdir)/data"
+
+EXTRA_DIST += src/cell.h src/hdf5-file.h src/image.h src/utils.h \
+              src/diffraction.h src/detector.h src/sfac.h src/reflections.h \
+              src/list_tmp.h src/statistics.h src/displaywindow.h \
+              src/render.h src/hdfsee.h src/dirax.h src/mosflm.h src/peaks.h \
+              src/index.h src/filters.h src/diffraction-gpu.h src/cl-utils.h \
+              src/symmetry.h src/povray.h src/index-priv.h src/geometry.h \
+              src/templates.h src/render_hkl.h src/stream.h src/thread-pool.h \
+              src/beam-parameters.h src/post-refinement.h src/hrs-scaling.h
+
+hdfseedir = $(datadir)/hdfsee
+hdfsee_DATA = data/displaywindow.ui
+
+crystfeldir = $(datadir)/crystfel
+crystfel_DATA = data/diffraction.cl data/defs.h data/sfac/Ca.nff \
+                data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
+                data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
+                data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat
+
+EXTRA_DIST += data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff \
+              data/sfac/H.nff data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
+              data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat \
+              data/defs.h data/diffraction.cl data/displaywindow.ui
+
+crystfeldocdir = $(docdir)
+crystfeldoc_DATA = doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
+                   doc/process_hkl.txt doc/symmetry.txt \
+                   doc/twin-calculator.pdf \
+                   doc/0-INDEX doc/examples/lcls-dec.geom \
+                   doc/examples/lcls-dec.beam \
+                   doc/examples/lcls-june-r0013-r0128.geom \
+                   doc/examples/lcls-june.beam \
+                   doc/examples/lcls-xpp-estimate.geom \
+                   doc/examples/lcls-xpp-estimate.beam \
+                   doc/examples/simple.geom
+
+EXTRA_DIST += doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
+              doc/process_hkl.txt doc/symmetry.txt doc/twin-calculator.pdf \
+              doc/0-INDEX doc/examples/lcls-dec.geom \
+              doc/examples/lcls-june-r0013-r0128.geom \
+              doc/examples/lcls-xpp-estimate.geom doc/examples/simple.geom
+
+scriptdir = $(docdir)/scripts
+script_DATA = scripts/check-near-bragg scripts/double-hit \
+              scripts/random-image scripts/stream-split scripts/wibbletron \
+              scripts/zone-axis scripts/create-mtz scripts/frequency \
+              scripts/i0-analysis scripts/mtz2hkl scripts/sequence-image \
+              scripts/test-facetron scripts/zone-axes \
+              scripts/alternate-stream scripts/README scripts/indexing-rate \
+              scripts/observed-peak-rate scripts/cell-please \
+              scripts/check-hkl-completeness.gp scripts/check-hkl-quality.gp \
+              scripts/compare-hkl.gp
+
+EXTRA_DIST += scripts/check-near-bragg scripts/double-hit scripts/random-image \
+              scripts/stream-split scripts/wibbletron scripts/zone-axis \
+              scripts/create-mtz scripts/frequency scripts/i0-analysis \
+              scripts/mtz2hkl scripts/sequence-image scripts/test-facetron \
+              scripts/zone-axes scripts/alternate-stream scripts/README \
+              scripts/indexing-rate scripts/observed-peak-rate \
+              scripts/cell-please scripts/check-hkl-completeness.gp \
+              scripts/check-hkl-quality.gp scripts/compare-hkl.gp
diff --git a/Makefile.in b/Makefile.in
index 0c556938..467a2308 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -14,6 +14,8 @@
 # PARTICULAR PURPOSE.
 
 @SET_MAKE@
+
+
 VPATH = @srcdir@
 pkgdatadir = $(datadir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
@@ -33,13 +35,23 @@ PRE_UNINSTALL = :
 POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
+bin_PROGRAMS = src/pattern_sim$(EXEEXT) src/process_hkl$(EXEEXT) \
+	src/get_hkl$(EXEEXT) src/indexamajig$(EXEEXT) \
+	src/compare_hkl$(EXEEXT) src/powder_plot$(EXEEXT) \
+	src/render_hkl$(EXEEXT) src/calibrate_detector$(EXEEXT) \
+	src/facetron$(EXEEXT) src/reintegrate$(EXEEXT) \
+	src/estimate_background$(EXEEXT) src/check_hkl$(EXEEXT) \
+	$(am__EXEEXT_1) $(am__EXEEXT_2)
+@HAVE_GTK_TRUE@am__append_1 = src/hdfsee
+@HAVE_CAIRO_TRUE@am__append_2 = src/cubeit
+@HAVE_OPENCL_TRUE@am__append_3 = src/diffraction-gpu.c src/cl-utils.c
+@HAVE_OPENCL_TRUE@am__append_4 = src/diffraction-gpu.c src/cl-utils.c
 subdir = .
 DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
 	$(srcdir)/Makefile.in $(srcdir)/config.h.in \
 	$(top_srcdir)/configure AUTHORS COPYING ChangeLog INSTALL NEWS \
-	build-aux/config.guess build-aux/config.sub build-aux/depcomp \
-	build-aux/install-sh build-aux/missing config.guess config.sub \
-	depcomp install-sh missing
+	build-aux/compile build-aux/config.guess build-aux/config.sub \
+	build-aux/depcomp build-aux/install-sh build-aux/missing
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/00gnulib.m4 \
 	$(top_srcdir)/m4/extensions.m4 \
@@ -59,14 +71,186 @@ mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = config.h
 CONFIG_CLEAN_FILES =
 CONFIG_CLEAN_VPATH_FILES =
-AM_V_GEN = $(am__v_GEN_$(V))
-am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
-am__v_GEN_0 = @echo "  GEN   " $@;
+@HAVE_GTK_TRUE@am__EXEEXT_1 = src/hdfsee$(EXEEXT)
+@HAVE_CAIRO_TRUE@am__EXEEXT_2 = src/cubeit$(EXEEXT)
+am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(crystfeldir)" \
+	"$(DESTDIR)$(crystfeldocdir)" "$(DESTDIR)$(hdfseedir)" \
+	"$(DESTDIR)$(scriptdir)"
+PROGRAMS = $(bin_PROGRAMS)
+am__dirstamp = $(am__leading_dot)dirstamp
+am_src_calibrate_detector_OBJECTS = src/calibrate_detector.$(OBJEXT) \
+	src/utils.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
+	src/image.$(OBJEXT) src/filters.$(OBJEXT) src/peaks.$(OBJEXT) \
+	src/detector.$(OBJEXT) src/cell.$(OBJEXT) \
+	src/thread-pool.$(OBJEXT)
+src_calibrate_detector_OBJECTS = $(am_src_calibrate_detector_OBJECTS)
+src_calibrate_detector_LDADD = $(LDADD)
+src_calibrate_detector_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_check_hkl_OBJECTS = src/check_hkl.$(OBJEXT) src/sfac.$(OBJEXT) \
+	src/cell.$(OBJEXT) src/utils.$(OBJEXT) \
+	src/reflections.$(OBJEXT) src/statistics.$(OBJEXT) \
+	src/symmetry.$(OBJEXT)
+src_check_hkl_OBJECTS = $(am_src_check_hkl_OBJECTS)
+src_check_hkl_LDADD = $(LDADD)
+src_check_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_compare_hkl_OBJECTS = src/compare_hkl.$(OBJEXT) \
+	src/sfac.$(OBJEXT) src/cell.$(OBJEXT) src/utils.$(OBJEXT) \
+	src/reflections.$(OBJEXT) src/statistics.$(OBJEXT) \
+	src/symmetry.$(OBJEXT)
+src_compare_hkl_OBJECTS = $(am_src_compare_hkl_OBJECTS)
+src_compare_hkl_LDADD = $(LDADD)
+src_compare_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am__src_cubeit_SOURCES_DIST = src/cubeit.c src/cell.c src/hdf5-file.c \
+	src/utils.c src/detector.c src/render.c src/filters.c \
+	src/image.c src/symmetry.c src/stream.c src/thread-pool.c
+@HAVE_CAIRO_TRUE@am_src_cubeit_OBJECTS = src/cubeit.$(OBJEXT) \
+@HAVE_CAIRO_TRUE@	src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
+@HAVE_CAIRO_TRUE@	src/utils.$(OBJEXT) src/detector.$(OBJEXT) \
+@HAVE_CAIRO_TRUE@	src/render.$(OBJEXT) src/filters.$(OBJEXT) \
+@HAVE_CAIRO_TRUE@	src/image.$(OBJEXT) src/symmetry.$(OBJEXT) \
+@HAVE_CAIRO_TRUE@	src/stream.$(OBJEXT) \
+@HAVE_CAIRO_TRUE@	src/thread-pool.$(OBJEXT)
+src_cubeit_OBJECTS = $(am_src_cubeit_OBJECTS)
+src_cubeit_LDADD = $(LDADD)
+src_cubeit_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_estimate_background_OBJECTS =  \
+	src/estimate_background.$(OBJEXT) src/stream.$(OBJEXT) \
+	src/utils.$(OBJEXT) src/cell.$(OBJEXT)
+src_estimate_background_OBJECTS =  \
+	$(am_src_estimate_background_OBJECTS)
+src_estimate_background_LDADD = $(LDADD)
+src_estimate_background_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_facetron_OBJECTS = src/facetron.$(OBJEXT) src/cell.$(OBJEXT) \
+	src/hdf5-file.$(OBJEXT) src/utils.$(OBJEXT) \
+	src/detector.$(OBJEXT) src/peaks.$(OBJEXT) src/image.$(OBJEXT) \
+	src/geometry.$(OBJEXT) src/reflections.$(OBJEXT) \
+	src/stream.$(OBJEXT) src/thread-pool.$(OBJEXT) \
+	src/beam-parameters.$(OBJEXT) src/symmetry.$(OBJEXT) \
+	src/post-refinement.$(OBJEXT) src/hrs-scaling.$(OBJEXT)
+src_facetron_OBJECTS = $(am_src_facetron_OBJECTS)
+src_facetron_LDADD = $(LDADD)
+src_facetron_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_get_hkl_OBJECTS = src/get_hkl.$(OBJEXT) src/sfac.$(OBJEXT) \
+	src/cell.$(OBJEXT) src/utils.$(OBJEXT) \
+	src/reflections.$(OBJEXT) src/symmetry.$(OBJEXT) \
+	src/beam-parameters.$(OBJEXT)
+src_get_hkl_OBJECTS = $(am_src_get_hkl_OBJECTS)
+src_get_hkl_LDADD = $(LDADD)
+src_get_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am__src_hdfsee_SOURCES_DIST = src/hdfsee.c src/displaywindow.c \
+	src/render.c src/hdf5-file.c src/utils.c src/image.c \
+	src/filters.c
+@HAVE_GTK_TRUE@am_src_hdfsee_OBJECTS = src/hdfsee.$(OBJEXT) \
+@HAVE_GTK_TRUE@	src/displaywindow.$(OBJEXT) \
+@HAVE_GTK_TRUE@	src/render.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
+@HAVE_GTK_TRUE@	src/utils.$(OBJEXT) src/image.$(OBJEXT) \
+@HAVE_GTK_TRUE@	src/filters.$(OBJEXT)
+src_hdfsee_OBJECTS = $(am_src_hdfsee_OBJECTS)
+src_hdfsee_LDADD = $(LDADD)
+src_hdfsee_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am__src_indexamajig_SOURCES_DIST = src/indexamajig.c src/hdf5-file.c \
+	src/utils.c src/cell.c src/image.c src/peaks.c src/index.c \
+	src/filters.c src/diffraction.c src/detector.c src/sfac.c \
+	src/dirax.c src/mosflm.c src/reflections.c src/templates.c \
+	src/symmetry.c src/geometry.c src/thread-pool.c \
+	src/beam-parameters.c src/diffraction-gpu.c src/cl-utils.c
+@HAVE_OPENCL_TRUE@am__objects_1 = src/diffraction-gpu.$(OBJEXT) \
+@HAVE_OPENCL_TRUE@	src/cl-utils.$(OBJEXT)
+am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT) \
+	src/hdf5-file.$(OBJEXT) src/utils.$(OBJEXT) src/cell.$(OBJEXT) \
+	src/image.$(OBJEXT) src/peaks.$(OBJEXT) src/index.$(OBJEXT) \
+	src/filters.$(OBJEXT) src/diffraction.$(OBJEXT) \
+	src/detector.$(OBJEXT) src/sfac.$(OBJEXT) src/dirax.$(OBJEXT) \
+	src/mosflm.$(OBJEXT) src/reflections.$(OBJEXT) \
+	src/templates.$(OBJEXT) src/symmetry.$(OBJEXT) \
+	src/geometry.$(OBJEXT) src/thread-pool.$(OBJEXT) \
+	src/beam-parameters.$(OBJEXT) $(am__objects_1)
+src_indexamajig_OBJECTS = $(am_src_indexamajig_OBJECTS)
+src_indexamajig_LDADD = $(LDADD)
+src_indexamajig_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am__src_pattern_sim_SOURCES_DIST = src/pattern_sim.c src/diffraction.c \
+	src/utils.c src/image.c src/cell.c src/hdf5-file.c \
+	src/detector.c src/sfac.c src/peaks.c src/reflections.c \
+	src/beam-parameters.c src/symmetry.c src/diffraction-gpu.c \
+	src/cl-utils.c
+am_src_pattern_sim_OBJECTS = src/pattern_sim.$(OBJEXT) \
+	src/diffraction.$(OBJEXT) src/utils.$(OBJEXT) \
+	src/image.$(OBJEXT) src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
+	src/detector.$(OBJEXT) src/sfac.$(OBJEXT) src/peaks.$(OBJEXT) \
+	src/reflections.$(OBJEXT) src/beam-parameters.$(OBJEXT) \
+	src/symmetry.$(OBJEXT) $(am__objects_1)
+src_pattern_sim_OBJECTS = $(am_src_pattern_sim_OBJECTS)
+src_pattern_sim_LDADD = $(LDADD)
+src_pattern_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_powder_plot_OBJECTS = src/powder_plot.$(OBJEXT) \
+	src/cell.$(OBJEXT) src/utils.$(OBJEXT) src/image.$(OBJEXT) \
+	src/hdf5-file.$(OBJEXT) src/detector.$(OBJEXT)
+src_powder_plot_OBJECTS = $(am_src_powder_plot_OBJECTS)
+src_powder_plot_LDADD = $(LDADD)
+src_powder_plot_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_process_hkl_OBJECTS = src/process_hkl.$(OBJEXT) \
+	src/sfac.$(OBJEXT) src/statistics.$(OBJEXT) src/cell.$(OBJEXT) \
+	src/utils.$(OBJEXT) src/reflections.$(OBJEXT) \
+	src/symmetry.$(OBJEXT) src/stream.$(OBJEXT) \
+	src/beam-parameters.$(OBJEXT)
+src_process_hkl_OBJECTS = $(am_src_process_hkl_OBJECTS)
+src_process_hkl_LDADD = $(LDADD)
+src_process_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_reintegrate_OBJECTS = src/reintegrate.$(OBJEXT) \
+	src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) src/utils.$(OBJEXT) \
+	src/detector.$(OBJEXT) src/peaks.$(OBJEXT) src/image.$(OBJEXT) \
+	src/stream.$(OBJEXT) src/index.$(OBJEXT) src/dirax.$(OBJEXT) \
+	src/mosflm.$(OBJEXT) src/templates.$(OBJEXT) \
+	src/geometry.$(OBJEXT) src/symmetry.$(OBJEXT) \
+	src/thread-pool.$(OBJEXT)
+src_reintegrate_OBJECTS = $(am_src_reintegrate_OBJECTS)
+src_reintegrate_LDADD = $(LDADD)
+src_reintegrate_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_render_hkl_OBJECTS = src/render_hkl.$(OBJEXT) \
+	src/cell.$(OBJEXT) src/reflections.$(OBJEXT) \
+	src/utils.$(OBJEXT) src/povray.$(OBJEXT) \
+	src/symmetry.$(OBJEXT) src/render.$(OBJEXT) \
+	src/hdf5-file.$(OBJEXT) src/image.$(OBJEXT) \
+	src/filters.$(OBJEXT)
+src_render_hkl_OBJECTS = $(am_src_render_hkl_OBJECTS)
+src_render_hkl_LDADD = $(LDADD)
+src_render_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+DEFAULT_INCLUDES = -I.@am__isrc@
+depcomp = $(SHELL) $(top_srcdir)/build-aux/depcomp
+am__depfiles_maybe = depfiles
+am__mv = mv -f
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_$(V))
+am__v_CC_ = $(am__v_CC_$(AM_DEFAULT_VERBOSITY))
+am__v_CC_0 = @echo "  CC    " $@;
 AM_V_at = $(am__v_at_$(V))
 am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))
 am__v_at_0 = @
-SOURCES =
-DIST_SOURCES =
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_$(V))
+am__v_CCLD_ = $(am__v_CCLD_$(AM_DEFAULT_VERBOSITY))
+am__v_CCLD_0 = @echo "  CCLD  " $@;
+AM_V_GEN = $(am__v_GEN_$(V))
+am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
+am__v_GEN_0 = @echo "  GEN   " $@;
+SOURCES = $(src_calibrate_detector_SOURCES) $(src_check_hkl_SOURCES) \
+	$(src_compare_hkl_SOURCES) $(src_cubeit_SOURCES) \
+	$(src_estimate_background_SOURCES) $(src_facetron_SOURCES) \
+	$(src_get_hkl_SOURCES) $(src_hdfsee_SOURCES) \
+	$(src_indexamajig_SOURCES) $(src_pattern_sim_SOURCES) \
+	$(src_powder_plot_SOURCES) $(src_process_hkl_SOURCES) \
+	$(src_reintegrate_SOURCES) $(src_render_hkl_SOURCES)
+DIST_SOURCES = $(src_calibrate_detector_SOURCES) \
+	$(src_check_hkl_SOURCES) $(src_compare_hkl_SOURCES) \
+	$(am__src_cubeit_SOURCES_DIST) \
+	$(src_estimate_background_SOURCES) $(src_facetron_SOURCES) \
+	$(src_get_hkl_SOURCES) $(am__src_hdfsee_SOURCES_DIST) \
+	$(am__src_indexamajig_SOURCES_DIST) \
+	$(am__src_pattern_sim_SOURCES_DIST) $(src_powder_plot_SOURCES) \
+	$(src_process_hkl_SOURCES) $(src_reintegrate_SOURCES) \
+	$(src_render_hkl_SOURCES)
 RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
 	html-recursive info-recursive install-data-recursive \
 	install-dvi-recursive install-exec-recursive \
@@ -74,6 +258,29 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
 	install-pdf-recursive install-ps-recursive install-recursive \
 	installcheck-recursive installdirs-recursive pdf-recursive \
 	ps-recursive uninstall-recursive
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+DATA = $(crystfel_DATA) $(crystfeldoc_DATA) $(hdfsee_DATA) \
+	$(script_DATA)
 RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
   distclean-recursive maintainer-clean-recursive
 AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
@@ -308,13 +515,131 @@ target_alias = @target_alias@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-EXTRA_DIST = configure m4/gnulib-cache.m4
-SUBDIRS = lib src data doc doc/examples scripts
+EXTRA_DIST = configure m4/gnulib-cache.m4 src/cell.h src/hdf5-file.h \
+	src/image.h src/utils.h src/diffraction.h src/detector.h \
+	src/sfac.h src/reflections.h src/list_tmp.h src/statistics.h \
+	src/displaywindow.h src/render.h src/hdfsee.h src/dirax.h \
+	src/mosflm.h src/peaks.h src/index.h src/filters.h \
+	src/diffraction-gpu.h src/cl-utils.h src/symmetry.h \
+	src/povray.h src/index-priv.h src/geometry.h src/templates.h \
+	src/render_hkl.h src/stream.h src/thread-pool.h \
+	src/beam-parameters.h src/post-refinement.h src/hrs-scaling.h \
+	data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff \
+	data/sfac/H.nff data/sfac/Mg.nff data/sfac/N.nff \
+	data/sfac/O.nff data/sfac/P.nff data/sfac/S.nff \
+	data/sfac/f0_WaasKirf.dat data/defs.h data/diffraction.cl \
+	data/displaywindow.ui doc/geometry.txt doc/indexamajig.txt \
+	doc/pattern_sim.txt doc/process_hkl.txt doc/symmetry.txt \
+	doc/twin-calculator.pdf doc/0-INDEX doc/examples/lcls-dec.geom \
+	doc/examples/lcls-june-r0013-r0128.geom \
+	doc/examples/lcls-xpp-estimate.geom doc/examples/simple.geom \
+	scripts/check-near-bragg scripts/double-hit \
+	scripts/random-image scripts/stream-split scripts/wibbletron \
+	scripts/zone-axis scripts/create-mtz scripts/frequency \
+	scripts/i0-analysis scripts/mtz2hkl scripts/sequence-image \
+	scripts/test-facetron scripts/zone-axes \
+	scripts/alternate-stream scripts/README scripts/indexing-rate \
+	scripts/observed-peak-rate scripts/cell-please \
+	scripts/check-hkl-completeness.gp scripts/check-hkl-quality.gp \
+	scripts/compare-hkl.gp
+SUBDIRS = lib
 ACLOCAL_AMFLAGS = -I m4
+AM_CFLAGS = -Wall
+AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -I$(top_srcdir)/lib
+LDADD = $(top_builddir)/lib/libgnu.a
+src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
+	src/utils.c src/image.c src/cell.c src/hdf5-file.c \
+	src/detector.c src/sfac.c src/peaks.c src/reflections.c \
+	src/beam-parameters.c src/symmetry.c $(am__append_3)
+src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c src/cell.c \
+                      src/utils.c src/reflections.c src/symmetry.c \
+                      src/stream.c src/beam-parameters.c
+
+src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c \
+	src/utils.c src/cell.c src/image.c src/peaks.c src/index.c \
+	src/filters.c src/diffraction.c src/detector.c src/sfac.c \
+	src/dirax.c src/mosflm.c src/reflections.c src/templates.c \
+	src/symmetry.c src/geometry.c src/thread-pool.c \
+	src/beam-parameters.c $(am__append_4)
+@HAVE_GTK_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/displaywindow.c src/render.c src/hdf5-file.c \
+@HAVE_GTK_TRUE@                 src/utils.c src/image.c src/filters.c
+
+src_get_hkl_SOURCES = src/get_hkl.c src/sfac.c src/cell.c src/utils.c \
+                  src/reflections.c src/symmetry.c src/beam-parameters.c
+
+src_compare_hkl_SOURCES = src/compare_hkl.c src/sfac.c src/cell.c src/utils.c \
+                      src/reflections.c src/statistics.c src/symmetry.c
+
+src_check_hkl_SOURCES = src/check_hkl.c src/sfac.c src/cell.c src/utils.c \
+                    src/reflections.c src/statistics.c src/symmetry.c
+
+src_powder_plot_SOURCES = src/powder_plot.c src/cell.c src/utils.c src/image.c \
+                      src/hdf5-file.c src/detector.c
+
+src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflections.c src/utils.c \
+                     src/povray.c src/symmetry.c src/render.c src/hdf5-file.c \
+                     src/image.c src/filters.c
+
+src_calibrate_detector_SOURCES = src/calibrate_detector.c src/utils.c \
+                             src/hdf5-file.c src/image.c src/filters.c \
+                             src/peaks.c src/detector.c src/cell.c \
+                             src/thread-pool.c
+
+src_facetron_SOURCES = src/facetron.c src/cell.c src/hdf5-file.c src/utils.c \
+                   src/detector.c src/peaks.c src/image.c src/geometry.c \
+                   src/reflections.c src/stream.c src/thread-pool.c \
+                   src/beam-parameters.c src/symmetry.c src/post-refinement.c \
+                   src/hrs-scaling.c
+
+@HAVE_CAIRO_TRUE@src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
+@HAVE_CAIRO_TRUE@                 src/detector.c src/render.c src/filters.c src/image.c \
+@HAVE_CAIRO_TRUE@                 src/symmetry.c src/stream.c src/thread-pool.c
+
+src_reintegrate_SOURCES = src/reintegrate.c src/cell.c src/hdf5-file.c src/utils.c \
+                      src/detector.c src/peaks.c src/image.c src/stream.c \
+                      src/index.c src/dirax.c src/mosflm.c src/templates.c \
+                      src/geometry.c src/symmetry.c src/thread-pool.c
+
+src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
+                              src/utils.c src/cell.c
+
+INCLUDES = "-I$(top_srcdir)/data"
+hdfseedir = $(datadir)/hdfsee
+hdfsee_DATA = data/displaywindow.ui
+crystfeldir = $(datadir)/crystfel
+crystfel_DATA = data/diffraction.cl data/defs.h data/sfac/Ca.nff \
+                data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
+                data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
+                data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat
+
+crystfeldocdir = $(docdir)
+crystfeldoc_DATA = doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
+                   doc/process_hkl.txt doc/symmetry.txt \
+                   doc/twin-calculator.pdf \
+                   doc/0-INDEX doc/examples/lcls-dec.geom \
+                   doc/examples/lcls-dec.beam \
+                   doc/examples/lcls-june-r0013-r0128.geom \
+                   doc/examples/lcls-june.beam \
+                   doc/examples/lcls-xpp-estimate.geom \
+                   doc/examples/lcls-xpp-estimate.beam \
+                   doc/examples/simple.geom
+
+scriptdir = $(docdir)/scripts
+script_DATA = scripts/check-near-bragg scripts/double-hit \
+              scripts/random-image scripts/stream-split scripts/wibbletron \
+              scripts/zone-axis scripts/create-mtz scripts/frequency \
+              scripts/i0-analysis scripts/mtz2hkl scripts/sequence-image \
+              scripts/test-facetron scripts/zone-axes \
+              scripts/alternate-stream scripts/README scripts/indexing-rate \
+              scripts/observed-peak-rate scripts/cell-please \
+              scripts/check-hkl-completeness.gp scripts/check-hkl-quality.gp \
+              scripts/compare-hkl.gp
+
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
 
 .SUFFIXES:
+.SUFFIXES: .c .o .obj
 am--refresh:
 	@:
 $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
@@ -366,6 +691,353 @@ $(srcdir)/config.h.in:  $(am__configure_deps)
 
 distclean-hdr:
 	-rm -f config.h stamp-h1
+install-binPROGRAMS: $(bin_PROGRAMS)
+	@$(NORMAL_INSTALL)
+	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	for p in $$list; do echo "$$p $$p"; done | \
+	sed 's/$(EXEEXT)$$//' | \
+	while read p p1; do if test -f $$p; \
+	  then echo "$$p"; echo "$$p"; else :; fi; \
+	done | \
+	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
+	sed 'N;N;N;s,\n, ,g' | \
+	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
+	    else { print "f", $$3 "/" $$4, $$1; } } \
+	  END { for (d in files) print "f", d, files[d] }' | \
+	while read type dir files; do \
+	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+	    test -z "$$files" || { \
+	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+	    } \
+	; done
+
+uninstall-binPROGRAMS:
+	@$(NORMAL_UNINSTALL)
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	files=`for p in $$list; do echo "$$p"; done | \
+	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
+	      -e 's/$$/$(EXEEXT)/' `; \
+	test -n "$$list" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(bindir)" && rm -f $$files
+
+clean-binPROGRAMS:
+	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+src/$(am__dirstamp):
+	@$(MKDIR_P) src
+	@: > src/$(am__dirstamp)
+src/$(DEPDIR)/$(am__dirstamp):
+	@$(MKDIR_P) src/$(DEPDIR)
+	@: > src/$(DEPDIR)/$(am__dirstamp)
+src/calibrate_detector.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/utils.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/hdf5-file.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/image.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/filters.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/peaks.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/detector.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/cell.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/thread-pool.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/calibrate_detector$(EXEEXT): $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/calibrate_detector$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_LDADD) $(LIBS)
+src/check_hkl.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/sfac.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/reflections.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/statistics.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/symmetry.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/check_hkl$(EXEEXT): $(src_check_hkl_OBJECTS) $(src_check_hkl_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/check_hkl$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_check_hkl_OBJECTS) $(src_check_hkl_LDADD) $(LIBS)
+src/compare_hkl.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/compare_hkl$(EXEEXT): $(src_compare_hkl_OBJECTS) $(src_compare_hkl_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/compare_hkl$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_compare_hkl_OBJECTS) $(src_compare_hkl_LDADD) $(LIBS)
+src/cubeit.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/render.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/stream.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/cubeit$(EXEEXT): $(src_cubeit_OBJECTS) $(src_cubeit_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/cubeit$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_cubeit_OBJECTS) $(src_cubeit_LDADD) $(LIBS)
+src/estimate_background.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/estimate_background$(EXEEXT): $(src_estimate_background_OBJECTS) $(src_estimate_background_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/estimate_background$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_estimate_background_OBJECTS) $(src_estimate_background_LDADD) $(LIBS)
+src/facetron.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/geometry.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/beam-parameters.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/post-refinement.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/hrs-scaling.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/facetron$(EXEEXT): $(src_facetron_OBJECTS) $(src_facetron_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/facetron$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_facetron_OBJECTS) $(src_facetron_LDADD) $(LIBS)
+src/get_hkl.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/get_hkl$(EXEEXT): $(src_get_hkl_OBJECTS) $(src_get_hkl_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/get_hkl$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_get_hkl_OBJECTS) $(src_get_hkl_LDADD) $(LIBS)
+src/hdfsee.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/displaywindow.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/hdfsee$(EXEEXT): $(src_hdfsee_OBJECTS) $(src_hdfsee_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/hdfsee$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_hdfsee_OBJECTS) $(src_hdfsee_LDADD) $(LIBS)
+src/indexamajig.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/index.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/diffraction.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/dirax.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/mosflm.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/templates.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/diffraction-gpu.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/cl-utils.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/indexamajig$(EXEEXT): $(src_indexamajig_OBJECTS) $(src_indexamajig_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/indexamajig$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_indexamajig_OBJECTS) $(src_indexamajig_LDADD) $(LIBS)
+src/pattern_sim.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/pattern_sim$(EXEEXT): $(src_pattern_sim_OBJECTS) $(src_pattern_sim_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/pattern_sim$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_pattern_sim_OBJECTS) $(src_pattern_sim_LDADD) $(LIBS)
+src/powder_plot.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/powder_plot$(EXEEXT): $(src_powder_plot_OBJECTS) $(src_powder_plot_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/powder_plot$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_powder_plot_OBJECTS) $(src_powder_plot_LDADD) $(LIBS)
+src/process_hkl.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/process_hkl$(EXEEXT): $(src_process_hkl_OBJECTS) $(src_process_hkl_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/process_hkl$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_process_hkl_OBJECTS) $(src_process_hkl_LDADD) $(LIBS)
+src/reintegrate.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/reintegrate$(EXEEXT): $(src_reintegrate_OBJECTS) $(src_reintegrate_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/reintegrate$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_reintegrate_OBJECTS) $(src_reintegrate_LDADD) $(LIBS)
+src/render_hkl.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/povray.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/render_hkl$(EXEEXT): $(src_render_hkl_OBJECTS) $(src_render_hkl_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/render_hkl$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_render_hkl_OBJECTS) $(src_render_hkl_LDADD) $(LIBS)
+
+mostlyclean-compile:
+	-rm -f *.$(OBJEXT)
+	-rm -f src/beam-parameters.$(OBJEXT)
+	-rm -f src/calibrate_detector.$(OBJEXT)
+	-rm -f src/cell.$(OBJEXT)
+	-rm -f src/check_hkl.$(OBJEXT)
+	-rm -f src/cl-utils.$(OBJEXT)
+	-rm -f src/compare_hkl.$(OBJEXT)
+	-rm -f src/cubeit.$(OBJEXT)
+	-rm -f src/detector.$(OBJEXT)
+	-rm -f src/diffraction-gpu.$(OBJEXT)
+	-rm -f src/diffraction.$(OBJEXT)
+	-rm -f src/dirax.$(OBJEXT)
+	-rm -f src/displaywindow.$(OBJEXT)
+	-rm -f src/estimate_background.$(OBJEXT)
+	-rm -f src/facetron.$(OBJEXT)
+	-rm -f src/filters.$(OBJEXT)
+	-rm -f src/geometry.$(OBJEXT)
+	-rm -f src/get_hkl.$(OBJEXT)
+	-rm -f src/hdf5-file.$(OBJEXT)
+	-rm -f src/hdfsee.$(OBJEXT)
+	-rm -f src/hrs-scaling.$(OBJEXT)
+	-rm -f src/image.$(OBJEXT)
+	-rm -f src/index.$(OBJEXT)
+	-rm -f src/indexamajig.$(OBJEXT)
+	-rm -f src/mosflm.$(OBJEXT)
+	-rm -f src/pattern_sim.$(OBJEXT)
+	-rm -f src/peaks.$(OBJEXT)
+	-rm -f src/post-refinement.$(OBJEXT)
+	-rm -f src/povray.$(OBJEXT)
+	-rm -f src/powder_plot.$(OBJEXT)
+	-rm -f src/process_hkl.$(OBJEXT)
+	-rm -f src/reflections.$(OBJEXT)
+	-rm -f src/reintegrate.$(OBJEXT)
+	-rm -f src/render.$(OBJEXT)
+	-rm -f src/render_hkl.$(OBJEXT)
+	-rm -f src/sfac.$(OBJEXT)
+	-rm -f src/statistics.$(OBJEXT)
+	-rm -f src/stream.$(OBJEXT)
+	-rm -f src/symmetry.$(OBJEXT)
+	-rm -f src/templates.$(OBJEXT)
+	-rm -f src/thread-pool.$(OBJEXT)
+	-rm -f src/utils.$(OBJEXT)
+
+distclean-compile:
+	-rm -f *.tab.c
+
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/beam-parameters.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/calibrate_detector.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cell.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/check_hkl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cl-utils.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/compare_hkl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cubeit.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/detector.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction-gpu.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/dirax.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/displaywindow.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/estimate_background.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/facetron.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/filters.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/geometry.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/get_hkl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hdf5-file.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hdfsee.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hrs-scaling.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/image.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/index.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/indexamajig.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/mosflm.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/pattern_sim.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/peaks.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/post-refinement.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/povray.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/powder_plot.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/process_hkl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflections.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reintegrate.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render_hkl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/sfac.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/statistics.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/stream.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/symmetry.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/templates.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/thread-pool.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/utils.Po@am__quote@
+
+.c.o:
+@am__fastdepCC_TRUE@	$(AM_V_CC)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.o$$||'`;\
+@am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ $< &&\
+@am__fastdepCC_TRUE@	$(am__mv) $$depbase.Tpo $$depbase.Po
+@am__fastdepCC_FALSE@	$(AM_V_CC) @AM_BACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@	$(COMPILE) -c -o $@ $<
+
+.c.obj:
+@am__fastdepCC_TRUE@	$(AM_V_CC)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.obj$$||'`;\
+@am__fastdepCC_TRUE@	$(COMPILE) -MT $@ -MD -MP -MF $$depbase.Tpo -c -o $@ `$(CYGPATH_W) '$<'` &&\
+@am__fastdepCC_TRUE@	$(am__mv) $$depbase.Tpo $$depbase.Po
+@am__fastdepCC_FALSE@	$(AM_V_CC) @AM_BACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@	$(COMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+install-crystfelDATA: $(crystfel_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(crystfeldir)" || $(MKDIR_P) "$(DESTDIR)$(crystfeldir)"
+	@list='$(crystfel_DATA)'; test -n "$(crystfeldir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(crystfeldir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(crystfeldir)" || exit $$?; \
+	done
+
+uninstall-crystfelDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(crystfel_DATA)'; test -n "$(crystfeldir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(crystfeldir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(crystfeldir)" && rm -f $$files
+install-crystfeldocDATA: $(crystfeldoc_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(crystfeldocdir)" || $(MKDIR_P) "$(DESTDIR)$(crystfeldocdir)"
+	@list='$(crystfeldoc_DATA)'; test -n "$(crystfeldocdir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(crystfeldocdir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(crystfeldocdir)" || exit $$?; \
+	done
+
+uninstall-crystfeldocDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(crystfeldoc_DATA)'; test -n "$(crystfeldocdir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(crystfeldocdir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(crystfeldocdir)" && rm -f $$files
+install-hdfseeDATA: $(hdfsee_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(hdfseedir)" || $(MKDIR_P) "$(DESTDIR)$(hdfseedir)"
+	@list='$(hdfsee_DATA)'; test -n "$(hdfseedir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(hdfseedir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(hdfseedir)" || exit $$?; \
+	done
+
+uninstall-hdfseeDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(hdfsee_DATA)'; test -n "$(hdfseedir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(hdfseedir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(hdfseedir)" && rm -f $$files
+install-scriptDATA: $(script_DATA)
+	@$(NORMAL_INSTALL)
+	test -z "$(scriptdir)" || $(MKDIR_P) "$(DESTDIR)$(scriptdir)"
+	@list='$(script_DATA)'; test -n "$(scriptdir)" || list=; \
+	for p in $$list; do \
+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(scriptdir)'"; \
+	  $(INSTALL_DATA) $$files "$(DESTDIR)$(scriptdir)" || exit $$?; \
+	done
+
+uninstall-scriptDATA:
+	@$(NORMAL_UNINSTALL)
+	@list='$(script_DATA)'; test -n "$(scriptdir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(scriptdir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(scriptdir)" && rm -f $$files
 
 # This directory's subdirectories are mostly independent; you can cd
 # into them and run `make' without going through this Makefile.
@@ -679,9 +1351,12 @@ distcleancheck: distclean
 	       exit 1; } >&2
 check-am: all-am
 check: check-recursive
-all-am: Makefile config.h
+all-am: Makefile $(PROGRAMS) $(DATA) config.h
 installdirs: installdirs-recursive
 installdirs-am:
+	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(crystfeldir)" "$(DESTDIR)$(crystfeldocdir)" "$(DESTDIR)$(hdfseedir)" "$(DESTDIR)$(scriptdir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
 install: install-recursive
 install-exec: install-exec-recursive
 install-data: install-data-recursive
@@ -703,18 +1378,22 @@ clean-generic:
 distclean-generic:
 	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
 	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+	-rm -f src/$(DEPDIR)/$(am__dirstamp)
+	-rm -f src/$(am__dirstamp)
 
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
 	@echo "it deletes files that may require special tools to rebuild."
 clean: clean-recursive
 
-clean-am: clean-generic mostlyclean-am
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
 
 distclean: distclean-recursive
 	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
+	-rm -rf src/$(DEPDIR)
 	-rm -f Makefile
-distclean-am: clean-am distclean-generic distclean-hdr distclean-tags
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-hdr distclean-tags
 
 dvi: dvi-recursive
 
@@ -728,13 +1407,14 @@ info: info-recursive
 
 info-am:
 
-install-data-am:
+install-data-am: install-crystfelDATA install-crystfeldocDATA \
+	install-hdfseeDATA install-scriptDATA
 
 install-dvi: install-dvi-recursive
 
 install-dvi-am:
 
-install-exec-am:
+install-exec-am: install-binPROGRAMS
 
 install-html: install-html-recursive
 
@@ -759,12 +1439,13 @@ installcheck-am:
 maintainer-clean: maintainer-clean-recursive
 	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
 	-rm -rf $(top_srcdir)/autom4te.cache
+	-rm -rf src/$(DEPDIR)
 	-rm -f Makefile
 maintainer-clean-am: distclean-am maintainer-clean-generic
 
 mostlyclean: mostlyclean-recursive
 
-mostlyclean-am: mostlyclean-generic
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
 
 pdf: pdf-recursive
 
@@ -774,25 +1455,33 @@ ps: ps-recursive
 
 ps-am:
 
-uninstall-am:
+uninstall-am: uninstall-binPROGRAMS uninstall-crystfelDATA \
+	uninstall-crystfeldocDATA uninstall-hdfseeDATA \
+	uninstall-scriptDATA
 
 .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
 	ctags-recursive install-am install-strip tags-recursive
 
 .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-	all all-am am--refresh check check-am clean clean-generic \
-	ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \
-	dist-lzma dist-shar dist-tarZ dist-xz dist-zip distcheck \
-	distclean distclean-generic distclean-hdr distclean-tags \
-	distcleancheck distdir distuninstallcheck dvi dvi-am html \
-	html-am info info-am install install-am install-data \
-	install-data-am install-dvi install-dvi-am install-exec \
-	install-exec-am install-html install-html-am install-info \
+	all all-am am--refresh check check-am clean clean-binPROGRAMS \
+	clean-generic ctags ctags-recursive dist dist-all dist-bzip2 \
+	dist-gzip dist-lzma dist-shar dist-tarZ dist-xz dist-zip \
+	distcheck distclean distclean-compile distclean-generic \
+	distclean-hdr distclean-tags distcleancheck distdir \
+	distuninstallcheck dvi dvi-am html html-am info info-am \
+	install install-am install-binPROGRAMS install-crystfelDATA \
+	install-crystfeldocDATA install-data install-data-am \
+	install-dvi install-dvi-am install-exec install-exec-am \
+	install-hdfseeDATA install-html install-html-am install-info \
 	install-info-am install-man install-pdf install-pdf-am \
-	install-ps install-ps-am install-strip installcheck \
-	installcheck-am installdirs installdirs-am maintainer-clean \
-	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
+	install-ps install-ps-am install-scriptDATA install-strip \
+	installcheck installcheck-am installdirs installdirs-am \
+	maintainer-clean maintainer-clean-generic mostlyclean \
+	mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
+	tags tags-recursive uninstall uninstall-am \
+	uninstall-binPROGRAMS uninstall-crystfelDATA \
+	uninstall-crystfeldocDATA uninstall-hdfseeDATA \
+	uninstall-scriptDATA
 
 
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/aclocal.m4 b/aclocal.m4
index a640ff7e..33582d0a 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1004,6 +1004,41 @@ AC_MSG_RESULT([$_am_result])
 rm -f confinc confmf
 ])
 
+# Copyright (C) 1999, 2000, 2001, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 6
+
+# AM_PROG_CC_C_O
+# --------------
+# Like AC_PROG_CC_C_O, but changed for automake.
+AC_DEFUN([AM_PROG_CC_C_O],
+[AC_REQUIRE([AC_PROG_CC_C_O])dnl
+AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([compile])dnl
+# FIXME: we rely on the cache variable name because
+# there is no other way.
+set dummy $CC
+am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
+   # Losing compiler, so override with the script.
+   # FIXME: It is wrong to rewrite CC.
+   # But if we don't then we get into trouble of one sort or another.
+   # A longer-term fix would be to have automake use am__CC in this case,
+   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+   CC="$am_aux_dir/compile $CC"
+fi
+dnl Make sure AC_PROG_CC is never called again, or it will override our
+dnl setting of CC.
+m4_define([AC_PROG_CC],
+          [m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])])
+])
+
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
 # Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
diff --git a/build-aux/compile b/build-aux/compile
new file mode 100755
index 00000000..c0096a7b
--- /dev/null
+++ b/build-aux/compile
@@ -0,0 +1,143 @@
+#! /bin/sh
+# Wrapper for compilers which do not understand `-c -o'.
+
+scriptversion=2009-10-06.20; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2009  Free Software
+# Foundation, Inc.
+# Written by Tom Tromey <tromey@cygnus.com>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+case $1 in
+  '')
+     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand `-c -o'.
+Remove `-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file `INSTALL'.
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "compile $scriptversion"
+    exit $?
+    ;;
+esac
+
+ofile=
+cfile=
+eat=
+
+for arg
+do
+  if test -n "$eat"; then
+    eat=
+  else
+    case $1 in
+      -o)
+	# configure might choose to run compile as `compile cc -o foo foo.c'.
+	# So we strip `-o arg' only if arg is an object.
+	eat=1
+	case $2 in
+	  *.o | *.obj)
+	    ofile=$2
+	    ;;
+	  *)
+	    set x "$@" -o "$2"
+	    shift
+	    ;;
+	esac
+	;;
+      *.c)
+	cfile=$1
+	set x "$@" "$1"
+	shift
+	;;
+      *)
+	set x "$@" "$1"
+	shift
+	;;
+    esac
+  fi
+  shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+  # If no `-o' option was seen then we might have been invoked from a
+  # pattern rule where we don't need one.  That is ok -- this is a
+  # normal compilation that the losing compiler can handle.  If no
+  # `.c' file was seen then we are probably linking.  That is also
+  # ok.
+  exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use `[/\\:.-]' here to ensure that we don't use the same name
+# that we are using for the .o file.  Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+  if mkdir "$lockdir" >/dev/null 2>&1; then
+    break
+  fi
+  sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/config.h.in b/config.h.in
index a1c63a32..0f412281 100644
--- a/config.h.in
+++ b/config.h.in
@@ -161,6 +161,9 @@
 /* Define to a substitute value for mmap()'s MAP_ANONYMOUS flag. */
 #undef MAP_ANONYMOUS
 
+/* Define to 1 if your C compiler doesn't accept -c and -o together. */
+#undef NO_MINUS_C_MINUS_O
+
 /* Name of package */
 #undef PACKAGE
 
diff --git a/configure b/configure
index cf817073..0cf3cf02 100755
--- a/configure
+++ b/configure
@@ -700,6 +700,8 @@ GNULIB_MEMCHR
 GL_COND_LIBTOOL_FALSE
 GL_COND_LIBTOOL_TRUE
 LIBOBJS
+AM_BACKSLASH
+AM_DEFAULT_VERBOSITY
 LN_S
 EGREP
 GREP
@@ -752,8 +754,6 @@ am__isrc
 INSTALL_DATA
 INSTALL_SCRIPT
 INSTALL_PROGRAM
-AM_BACKSLASH
-AM_DEFAULT_VERBOSITY
 target_alias
 host_alias
 build_alias
@@ -795,8 +795,8 @@ SHELL'
 ac_subst_files=''
 ac_user_opts='
 enable_option_checking
-enable_silent_rules
 enable_dependency_tracking
+enable_silent_rules
 with_hdf5
 with_gsl
 enable_opencl
@@ -1440,10 +1440,10 @@ Optional Features:
   --disable-option-checking  ignore unrecognized --enable/--with options
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --enable-silent-rules          less verbose build output (undo: `make V=1')
-  --disable-silent-rules         verbose build output (undo: `make V=0')
   --disable-dependency-tracking  speeds up one-time build
   --enable-dependency-tracking   do not reject slow dependency extractors
+  --enable-silent-rules          less verbose build output (undo: `make V=1')
+  --disable-silent-rules         verbose build output (undo: `make V=0')
   --enable-opencl         Enable the use of OpenCL
   --disable-gtk           Disable GTK+/GLib
   --disable-gtktest       do not try to compile and run a test GTK+ program
@@ -2304,19 +2304,6 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
-# Check whether --enable-silent-rules was given.
-if test "${enable_silent_rules+set}" = set; then :
-  enableval=$enable_silent_rules;
-fi
-
-case $enable_silent_rules in
-yes) AM_DEFAULT_VERBOSITY=0;;
-no)  AM_DEFAULT_VERBOSITY=1;;
-*)   AM_DEFAULT_VERBOSITY=0;;
-esac
-AM_BACKSLASH='\'
-
-VERSION=0.2.0
 ac_aux_dir=
 for ac_dir in build-aux "$srcdir"/build-aux; do
   for ac_t in install-sh install.sh shtool; do
@@ -2340,7 +2327,6 @@ ac_config_sub="$SHELL $ac_aux_dir/config.sub"  # Please don't use this var.
 ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.
 
 
-
 ac_config_headers="$ac_config_headers config.h"
 
 am__api_version='1.11'
@@ -2781,8 +2767,8 @@ fi
 
 
 # Define the identity of the package.
- PACKAGE=crystfel
- VERSION="$VERSION"
+ PACKAGE='crystfel'
+ VERSION='0.2.0'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -4456,6 +4442,132 @@ $as_echo "$ac_cv_safe_to_define___extensions__" >&6; }
   # Code from module strnlen:
   # Code from module warn-on-use:
 
+if test "x$CC" != xcc; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC and cc understand -c and -o together" >&5
+$as_echo_n "checking whether $CC and cc understand -c and -o together... " >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether cc understands -c and -o together" >&5
+$as_echo_n "checking whether cc understands -c and -o together... " >&6; }
+fi
+set dummy $CC; ac_cc=`$as_echo "$2" |
+		      sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+if { as_var=ac_cv_prog_cc_${ac_cc}_c_o; eval "test \"\${$as_var+set}\" = set"; }; then :
+  $as_echo_n "(cached) " >&6
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+# Make sure it works both with $CC and with simple cc.
+# We do the test twice because some compilers refuse to overwrite an
+# existing .o file with -o, though they will create one.
+ac_try='$CC -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
+rm -f conftest2.*
+if { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; } &&
+   test -f conftest2.$ac_objext && { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; };
+then
+  eval ac_cv_prog_cc_${ac_cc}_c_o=yes
+  if test "x$CC" != xcc; then
+    # Test first that cc exists at all.
+    if { ac_try='cc -c conftest.$ac_ext >&5'
+  { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }; }; then
+      ac_try='cc -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
+      rm -f conftest2.*
+      if { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; } &&
+	 test -f conftest2.$ac_objext && { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; };
+      then
+	# cc works too.
+	:
+      else
+	# cc exists but doesn't like -o.
+	eval ac_cv_prog_cc_${ac_cc}_c_o=no
+      fi
+    fi
+  fi
+else
+  eval ac_cv_prog_cc_${ac_cc}_c_o=no
+fi
+rm -f core conftest*
+
+fi
+if eval test \$ac_cv_prog_cc_${ac_cc}_c_o = yes; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+
+$as_echo "#define NO_MINUS_C_MINUS_O 1" >>confdefs.h
+
+fi
+
+# FIXME: we rely on the cache variable name because
+# there is no other way.
+set dummy $CC
+am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
+   # Losing compiler, so override with the script.
+   # FIXME: It is wrong to rewrite CC.
+   # But if we don't then we get into trouble of one sort or another.
+   # A longer-term fix would be to have automake use am__CC in this case,
+   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+   CC="$am_aux_dir/compile $CC"
+fi
+
+
 for ac_prog in gawk mawk nawk awk
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
@@ -4602,6 +4714,17 @@ else
   RANLIB="$ac_cv_prog_RANLIB"
 fi
 
+# Check whether --enable-silent-rules was given.
+if test "${enable_silent_rules+set}" = set; then :
+  enableval=$enable_silent_rules;
+fi
+
+case $enable_silent_rules in
+yes) AM_DEFAULT_VERBOSITY=0;;
+no)  AM_DEFAULT_VERBOSITY=1;;
+*)   AM_DEFAULT_VERBOSITY=0;;
+esac
+AM_BACKSLASH='\'
 
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
@@ -6797,9 +6920,7 @@ CFLAGS="$CFLAGS $LIBTIFF_CFLAGS -D_GNU_SOURCE $libPNG_CFLAGS $Cairo_CFLAGS"
 LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
 LIBS="$LIBS $LIBTIFF_LIBS $libPNG_LIBS $Cairo_LIBS"
 
-ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile doc/Makefile"
-
-ac_config_files="$ac_config_files scripts/Makefile doc/examples/Makefile lib/Makefile"
+ac_config_files="$ac_config_files Makefile lib/Makefile"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -7562,11 +7683,6 @@ do
     "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-    "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
-    "data/Makefile") CONFIG_FILES="$CONFIG_FILES data/Makefile" ;;
-    "doc/Makefile") CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;;
-    "scripts/Makefile") CONFIG_FILES="$CONFIG_FILES scripts/Makefile" ;;
-    "doc/examples/Makefile") CONFIG_FILES="$CONFIG_FILES doc/examples/Makefile" ;;
     "lib/Makefile") CONFIG_FILES="$CONFIG_FILES lib/Makefile" ;;
 
   *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
diff --git a/configure.ac b/configure.ac
index 499957cf..e4fb4bed 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,20 +1,18 @@
 dnl Process this file with autoconf to produce a configure script.
 
 AC_INIT(crystfel, 0.2.0, taw@physics.org)
-AM_SILENT_RULES([yes])
-VERSION=AC_PACKAGE_VERSION
 AC_CONFIG_AUX_DIR([build-aux])
-
 AM_CONFIG_HEADER(config.h)
-AM_INIT_AUTOMAKE(crystfel, "$VERSION")
+AM_INIT_AUTOMAKE([subdir-objects])
 
 AC_PROG_CC
 gl_EARLY
+AM_PROG_CC_C_O
 AC_PROG_AWK
 AC_PROG_INSTALL
 AC_PROG_LN_S
 AC_PROG_RANLIB
-
+AM_SILENT_RULES([yes])
 
 AC_HEADER_STDC
 AC_CHECK_HEADERS([fcntl.h stdlib.h unistd.h])
@@ -151,6 +149,5 @@ CFLAGS="$CFLAGS $LIBTIFF_CFLAGS -D_GNU_SOURCE $libPNG_CFLAGS $Cairo_CFLAGS"
 LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
 LIBS="$LIBS $LIBTIFF_LIBS $libPNG_LIBS $Cairo_LIBS"
 
-AC_CONFIG_FILES(Makefile src/Makefile data/Makefile doc/Makefile)
-AC_CONFIG_FILES(scripts/Makefile doc/examples/Makefile lib/Makefile)
+AC_CONFIG_FILES(Makefile lib/Makefile)
 AC_OUTPUT
diff --git a/data/Makefile.am b/data/Makefile.am
deleted file mode 100644
index 75c18c64..00000000
--- a/data/Makefile.am
+++ /dev/null
@@ -1,11 +0,0 @@
-hdfseedir = $(datadir)/hdfsee
-hdfsee_DATA = displaywindow.ui
-
-crystfeldir = $(datadir)/crystfel
-crystfel_DATA = diffraction.cl defs.h sfac/Ca.nff sfac/C.nff sfac/Fe.nff \
-                sfac/H.nff sfac/Mg.nff sfac/N.nff sfac/O.nff sfac/P.nff \
-                sfac/S.nff sfac/f0_WaasKirf.dat
-
-EXTRA_DIST = sfac/Ca.nff sfac/C.nff sfac/Fe.nff sfac/H.nff  sfac/Mg.nff \
-             sfac/N.nff sfac/O.nff sfac/P.nff sfac/S.nff sfac/f0_WaasKirf.dat \
-             defs.h diffraction.cl displaywindow.ui
diff --git a/data/Makefile.in b/data/Makefile.in
deleted file mode 100644
index 7eac4b2d..00000000
--- a/data/Makefile.in
+++ /dev/null
@@ -1,514 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-# PARTICULAR PURPOSE.
-
-@SET_MAKE@
-
-VPATH = @srcdir@
-pkgdatadir = $(datadir)/@PACKAGE@
-pkgincludedir = $(includedir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
-pkglibexecdir = $(libexecdir)/@PACKAGE@
-am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
-install_sh_DATA = $(install_sh) -c -m 644
-install_sh_PROGRAM = $(install_sh) -c
-install_sh_SCRIPT = $(install_sh) -c
-INSTALL_HEADER = $(INSTALL_DATA)
-transform = $(program_transform_name)
-NORMAL_INSTALL = :
-PRE_INSTALL = :
-POST_INSTALL = :
-NORMAL_UNINSTALL = :
-PRE_UNINSTALL = :
-POST_UNINSTALL = :
-build_triplet = @build@
-host_triplet = @host@
-subdir = data
-DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
-ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/m4/00gnulib.m4 \
-	$(top_srcdir)/m4/extensions.m4 \
-	$(top_srcdir)/m4/gnulib-common.m4 \
-	$(top_srcdir)/m4/gnulib-comp.m4 \
-	$(top_srcdir)/m4/include_next.m4 $(top_srcdir)/m4/memchr.m4 \
-	$(top_srcdir)/m4/mmap-anon.m4 $(top_srcdir)/m4/onceonly.m4 \
-	$(top_srcdir)/m4/stddef_h.m4 $(top_srcdir)/m4/string_h.m4 \
-	$(top_srcdir)/m4/strndup.m4 $(top_srcdir)/m4/strnlen.m4 \
-	$(top_srcdir)/m4/warn-on-use.m4 $(top_srcdir)/m4/wchar_t.m4 \
-	$(top_srcdir)/configure.ac
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
-	$(ACLOCAL_M4)
-mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/config.h
-CONFIG_CLEAN_FILES =
-CONFIG_CLEAN_VPATH_FILES =
-AM_V_GEN = $(am__v_GEN_$(V))
-am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
-am__v_GEN_0 = @echo "  GEN   " $@;
-AM_V_at = $(am__v_at_$(V))
-am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))
-am__v_at_0 = @
-SOURCES =
-DIST_SOURCES =
-am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-am__vpath_adj = case $$p in \
-    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-    *) f=$$p;; \
-  esac;
-am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-am__install_max = 40
-am__nobase_strip_setup = \
-  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-am__nobase_strip = \
-  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-am__nobase_list = $(am__nobase_strip_setup); \
-  for p in $$list; do echo "$$p $$p"; done | \
-  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-    if (++n[$$2] == $(am__install_max)) \
-      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-    END { for (dir in files) print dir, files[dir] }'
-am__base_list = \
-  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(crystfeldir)" "$(DESTDIR)$(hdfseedir)"
-DATA = $(crystfel_DATA) $(hdfsee_DATA)
-DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = @ACLOCAL@
-AMTAR = @AMTAR@
-AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
-AUTOCONF = @AUTOCONF@
-AUTOHEADER = @AUTOHEADER@
-AUTOMAKE = @AUTOMAKE@
-AWK = @AWK@
-CC = @CC@
-CCDEPMODE = @CCDEPMODE@
-CFLAGS = @CFLAGS@
-CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
-CYGPATH_W = @CYGPATH_W@
-Cairo_CFLAGS = @Cairo_CFLAGS@
-Cairo_LIBS = @Cairo_LIBS@
-DEFS = @DEFS@
-DEPDIR = @DEPDIR@
-ECHO_C = @ECHO_C@
-ECHO_N = @ECHO_N@
-ECHO_T = @ECHO_T@
-EGREP = @EGREP@
-EXEEXT = @EXEEXT@
-GNULIB_MBSCASECMP = @GNULIB_MBSCASECMP@
-GNULIB_MBSCASESTR = @GNULIB_MBSCASESTR@
-GNULIB_MBSCHR = @GNULIB_MBSCHR@
-GNULIB_MBSCSPN = @GNULIB_MBSCSPN@
-GNULIB_MBSLEN = @GNULIB_MBSLEN@
-GNULIB_MBSNCASECMP = @GNULIB_MBSNCASECMP@
-GNULIB_MBSNLEN = @GNULIB_MBSNLEN@
-GNULIB_MBSPBRK = @GNULIB_MBSPBRK@
-GNULIB_MBSPCASECMP = @GNULIB_MBSPCASECMP@
-GNULIB_MBSRCHR = @GNULIB_MBSRCHR@
-GNULIB_MBSSEP = @GNULIB_MBSSEP@
-GNULIB_MBSSPN = @GNULIB_MBSSPN@
-GNULIB_MBSSTR = @GNULIB_MBSSTR@
-GNULIB_MBSTOK_R = @GNULIB_MBSTOK_R@
-GNULIB_MEMCHR = @GNULIB_MEMCHR@
-GNULIB_MEMMEM = @GNULIB_MEMMEM@
-GNULIB_MEMPCPY = @GNULIB_MEMPCPY@
-GNULIB_MEMRCHR = @GNULIB_MEMRCHR@
-GNULIB_RAWMEMCHR = @GNULIB_RAWMEMCHR@
-GNULIB_STPCPY = @GNULIB_STPCPY@
-GNULIB_STPNCPY = @GNULIB_STPNCPY@
-GNULIB_STRCASESTR = @GNULIB_STRCASESTR@
-GNULIB_STRCHRNUL = @GNULIB_STRCHRNUL@
-GNULIB_STRDUP = @GNULIB_STRDUP@
-GNULIB_STRERROR = @GNULIB_STRERROR@
-GNULIB_STRERROR_R = @GNULIB_STRERROR_R@
-GNULIB_STRNCAT = @GNULIB_STRNCAT@
-GNULIB_STRNDUP = @GNULIB_STRNDUP@
-GNULIB_STRNLEN = @GNULIB_STRNLEN@
-GNULIB_STRPBRK = @GNULIB_STRPBRK@
-GNULIB_STRSEP = @GNULIB_STRSEP@
-GNULIB_STRSIGNAL = @GNULIB_STRSIGNAL@
-GNULIB_STRSTR = @GNULIB_STRSTR@
-GNULIB_STRTOK_R = @GNULIB_STRTOK_R@
-GNULIB_STRVERSCMP = @GNULIB_STRVERSCMP@
-GREP = @GREP@
-GTK_CFLAGS = @GTK_CFLAGS@
-GTK_LIBS = @GTK_LIBS@
-HAVE_DECL_MEMMEM = @HAVE_DECL_MEMMEM@
-HAVE_DECL_MEMRCHR = @HAVE_DECL_MEMRCHR@
-HAVE_DECL_STRDUP = @HAVE_DECL_STRDUP@
-HAVE_DECL_STRERROR_R = @HAVE_DECL_STRERROR_R@
-HAVE_DECL_STRNDUP = @HAVE_DECL_STRNDUP@
-HAVE_DECL_STRNLEN = @HAVE_DECL_STRNLEN@
-HAVE_DECL_STRSIGNAL = @HAVE_DECL_STRSIGNAL@
-HAVE_DECL_STRTOK_R = @HAVE_DECL_STRTOK_R@
-HAVE_MBSLEN = @HAVE_MBSLEN@
-HAVE_MEMCHR = @HAVE_MEMCHR@
-HAVE_MEMPCPY = @HAVE_MEMPCPY@
-HAVE_RAWMEMCHR = @HAVE_RAWMEMCHR@
-HAVE_STPCPY = @HAVE_STPCPY@
-HAVE_STPNCPY = @HAVE_STPNCPY@
-HAVE_STRCASESTR = @HAVE_STRCASESTR@
-HAVE_STRCHRNUL = @HAVE_STRCHRNUL@
-HAVE_STRPBRK = @HAVE_STRPBRK@
-HAVE_STRSEP = @HAVE_STRSEP@
-HAVE_STRVERSCMP = @HAVE_STRVERSCMP@
-HAVE_WCHAR_T = @HAVE_WCHAR_T@
-INCLUDE_NEXT = @INCLUDE_NEXT@
-INCLUDE_NEXT_AS_FIRST_DIRECTIVE = @INCLUDE_NEXT_AS_FIRST_DIRECTIVE@
-INSTALL = @INSTALL@
-INSTALL_DATA = @INSTALL_DATA@
-INSTALL_PROGRAM = @INSTALL_PROGRAM@
-INSTALL_SCRIPT = @INSTALL_SCRIPT@
-INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = @LDFLAGS@
-LIBGNU_LIBDEPS = @LIBGNU_LIBDEPS@
-LIBGNU_LTLIBDEPS = @LIBGNU_LTLIBDEPS@
-LIBOBJS = @LIBOBJS@
-LIBS = @LIBS@
-LN_S = @LN_S@
-LTLIBOBJS = @LTLIBOBJS@
-MAKEINFO = @MAKEINFO@
-MKDIR_P = @MKDIR_P@
-NEXT_AS_FIRST_DIRECTIVE_STDDEF_H = @NEXT_AS_FIRST_DIRECTIVE_STDDEF_H@
-NEXT_AS_FIRST_DIRECTIVE_STRING_H = @NEXT_AS_FIRST_DIRECTIVE_STRING_H@
-NEXT_STDDEF_H = @NEXT_STDDEF_H@
-NEXT_STRING_H = @NEXT_STRING_H@
-OBJEXT = @OBJEXT@
-PACKAGE = @PACKAGE@
-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
-PACKAGE_NAME = @PACKAGE_NAME@
-PACKAGE_STRING = @PACKAGE_STRING@
-PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
-PACKAGE_VERSION = @PACKAGE_VERSION@
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