Recurse into 'lib' first; Update makefiles

6 files changed, 23 insertions, 1512 deletions

diff --git a/Makefile.am b/Makefile.am
index 6f0911cd..7e6224bd 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,3 +1,3 @@
 EXTRA_DIST = configure m4/gnulib-cache.m4
-SUBDIRS = src data doc doc/examples scripts lib
+SUBDIRS = lib src data doc doc/examples scripts
 ACLOCAL_AMFLAGS = -I m4
diff --git a/Makefile.in b/Makefile.in
index 1dd25b25..a9245228 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -307,7 +307,7 @@ top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 EXTRA_DIST = configure m4/gnulib-cache.m4
-SUBDIRS = src data doc doc/examples scripts lib
+SUBDIRS = lib src data doc doc/examples scripts
 ACLOCAL_AMFLAGS = -I m4
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
diff --git a/configure b/configure
index 719913b4..38d96fc4 100755
--- a/configure
+++ b/configure
@@ -2823,9 +2823,6 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
 
 
 
-ac_config_files="$ac_config_files lib/Makefile"
-
-
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
 ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -6793,1492 +6790,9 @@ 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 scripts/Makefile"
-
-cat >confcache <<\_ACEOF
-# This file is a shell script that caches the results of configure
-# tests run on this system so they can be shared between configure
-# scripts and configure runs, see configure's option --config-cache.
-# It is not useful on other systems.  If it contains results you don't
-# want to keep, you may remove or edit it.
-#
-# config.status only pays attention to the cache file if you give it
-# the --recheck option to rerun configure.
-#
-# `ac_cv_env_foo' variables (set or unset) will be overridden when
-# loading this file, other *unset* `ac_cv_foo' will be assigned the
-# following values.
-
-_ACEOF
-
-# The following way of writing the cache mishandles newlines in values,
-# but we know of no workaround that is simple, portable, and efficient.
-# So, we kill variables containing newlines.
-# Ultrix sh set writes to stderr and can't be redirected directly,
-# and sets the high bit in the cache file unless we assign to the vars.
-(
-  for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
-    eval ac_val=\$$ac_var
-    case $ac_val in #(
-    *${as_nl}*)
-      case $ac_var in #(
-      *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
-$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
-      esac
-      case $ac_var in #(
-      _ | IFS | as_nl) ;; #(
-      BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
-      *) { eval $ac_var=; unset $ac_var;} ;;
-      esac ;;
-    esac
-  done
-
-  (set) 2>&1 |
-    case $as_nl`(ac_space=' '; set) 2>&1` in #(
-    *${as_nl}ac_space=\ *)
-      # `set' does not quote correctly, so add quotes: double-quote
-      # substitution turns \\\\ into \\, and sed turns \\ into \.
-      sed -n \
-	"s/'/'\\\\''/g;
-	  s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
-      ;; #(
-    *)
-      # `set' quotes correctly as required by POSIX, so do not add quotes.
-      sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
-      ;;
-    esac |
-    sort
-) |
-  sed '
-     /^ac_cv_env_/b end
-     t clear
-     :clear
-     s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
-     t end
-     s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
-     :end' >>confcache
-if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
-  if test -w "$cache_file"; then
-    test "x$cache_file" != "x/dev/null" &&
-      { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
-$as_echo "$as_me: updating cache $cache_file" >&6;}
-    cat confcache >$cache_file
-  else
-    { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
-$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
-  fi
-fi
-rm -f confcache
-
-test "x$prefix" = xNONE && prefix=$ac_default_prefix
-# Let make expand exec_prefix.
-test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile doc/Makefile"
 
-DEFS=-DHAVE_CONFIG_H
-
-ac_libobjs=
-ac_ltlibobjs=
-for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
-  # 1. Remove the extension, and $U if already installed.
-  ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
-  ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
-  # 2. Prepend LIBOBJDIR.  When used with automake>=1.10 LIBOBJDIR
-  #    will be set to the directory where LIBOBJS objects are built.
-  as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
-  as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
-done
-LIBOBJS=$ac_libobjs
-
-LTLIBOBJS=$ac_ltlibobjs
-
-
- if test -n "$EXEEXT"; then
-  am__EXEEXT_TRUE=
-  am__EXEEXT_FALSE='#'
-else
-  am__EXEEXT_TRUE='#'
-  am__EXEEXT_FALSE=
-fi
-
-if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
-  as_fn_error "conditional \"AMDEP\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
-  as_fn_error "conditional \"am__fastdepCC\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${GL_COND_LIBTOOL_TRUE}" && test -z "${GL_COND_LIBTOOL_FALSE}"; then
-  as_fn_error "conditional \"GL_COND_LIBTOOL\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-
-    gl_libobjs=
-    gl_ltlibobjs=
-    if test -n "$gl_LIBOBJS"; then
-      # Remove the extension.
-      sed_drop_objext='s/\.o$//;s/\.obj$//'
-      for i in `for i in $gl_LIBOBJS; do echo "$i"; done | sed -e "$sed_drop_objext" | sort | uniq`; do
-        gl_libobjs="$gl_libobjs $i.$ac_objext"
-        gl_ltlibobjs="$gl_ltlibobjs $i.lo"
-      done
-    fi
-    gl_LIBOBJS=$gl_libobjs
-
-    gl_LTLIBOBJS=$gl_ltlibobjs
-
-
-
-    gltests_libobjs=
-    gltests_ltlibobjs=
-    if test -n "$gltests_LIBOBJS"; then
-      # Remove the extension.
-      sed_drop_objext='s/\.o$//;s/\.obj$//'
-      for i in `for i in $gltests_LIBOBJS; do echo "$i"; done | sed -e "$sed_drop_objext" | sort | uniq`; do
-        gltests_libobjs="$gltests_libobjs $i.$ac_objext"
-        gltests_ltlibobjs="$gltests_ltlibobjs $i.lo"
-      done
-    fi
-    gltests_LIBOBJS=$gltests_libobjs
-
-    gltests_LTLIBOBJS=$gltests_ltlibobjs
-
-
-if test -z "${HAVE_OPENCL_TRUE}" && test -z "${HAVE_OPENCL_FALSE}"; then
-  as_fn_error "conditional \"HAVE_OPENCL\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${HAVE_GTK_TRUE}" && test -z "${HAVE_GTK_FALSE}"; then
-  as_fn_error "conditional \"HAVE_GTK\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${HAVE_CAIRO_TRUE}" && test -z "${HAVE_CAIRO_FALSE}"; then
-  as_fn_error "conditional \"HAVE_CAIRO\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-
-: ${CONFIG_STATUS=./config.status}
-ac_write_fail=0
-ac_clean_files_save=$ac_clean_files
-ac_clean_files="$ac_clean_files $CONFIG_STATUS"
-{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
-$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
-as_write_fail=0
-cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
-#! $SHELL
-# Generated by $as_me.
-# Run this file to recreate the current configuration.
-# Compiler output produced by configure, useful for debugging
-# configure, is in config.log if it exists.
-
-debug=false
-ac_cs_recheck=false
-ac_cs_silent=false
-
-SHELL=\${CONFIG_SHELL-$SHELL}
-export SHELL
-_ASEOF
-cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
-## -------------------- ##
-## M4sh Initialization. ##
-## -------------------- ##
-
-# Be more Bourne compatible
-DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
-  emulate sh
-  NULLCMD=:
-  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
-  # is contrary to our usage.  Disable this feature.
-  alias -g '${1+"$@"}'='"$@"'
-  setopt NO_GLOB_SUBST
-else
-  case `(set -o) 2>/dev/null` in #(
-  *posix*) :
-    set -o posix ;; #(
-  *) :
-     ;;
-esac
-fi
-
-
-as_nl='
-'
-export as_nl
-# Printing a long string crashes Solaris 7 /usr/bin/printf.
-as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-# Prefer a ksh shell builtin over an external printf program on Solaris,
-# but without wasting forks for bash or zsh.
-if test -z "$BASH_VERSION$ZSH_VERSION" \
-    && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
-  as_echo='print -r --'
-  as_echo_n='print -rn --'
-elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
-  as_echo='printf %s\n'
-  as_echo_n='printf %s'
-else
-  if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
-    as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
-    as_echo_n='/usr/ucb/echo -n'
-  else
-    as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
-    as_echo_n_body='eval
-      arg=$1;
-      case $arg in #(
-      *"$as_nl"*)
-	expr "X$arg" : "X\\(.*\\)$as_nl";
-	arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
-      esac;
-      expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
-    '
-    export as_echo_n_body
-    as_echo_n='sh -c $as_echo_n_body as_echo'
-  fi
-  export as_echo_body
-  as_echo='sh -c $as_echo_body as_echo'
-fi
-
-# The user is always right.
-if test "${PATH_SEPARATOR+set}" != set; then
-  PATH_SEPARATOR=:
-  (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
-    (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
-      PATH_SEPARATOR=';'
-  }
-fi
-
-
-# IFS
-# We need space, tab and new line, in precisely that order.  Quoting is
-# there to prevent editors from complaining about space-tab.
-# (If _AS_PATH_WALK were called with IFS unset, it would disable word
-# splitting by setting IFS to empty value.)
-IFS=" ""	$as_nl"
-
-# Find who we are.  Look in the path if we contain no directory separator.
-case $0 in #((
-  *[\\/]* ) as_myself=$0 ;;
-  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
-  IFS=$as_save_IFS
-  test -z "$as_dir" && as_dir=.
-    test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
-  done
-IFS=$as_save_IFS
-
-     ;;
-esac
-# We did not find ourselves, most probably we were run as `sh COMMAND'
-# in which case we are not to be found in the path.
-if test "x$as_myself" = x; then
-  as_myself=$0
-fi
-if test ! -f "$as_myself"; then
-  $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
-  exit 1
-fi
-
-# Unset variables that we do not need and which cause bugs (e.g. in
-# pre-3.0 UWIN ksh).  But do not cause bugs in bash 2.01; the "|| exit 1"
-# suppresses any "Segmentation fault" message there.  '((' could
-# trigger a bug in pdksh 5.2.14.
-for as_var in BASH_ENV ENV MAIL MAILPATH
-do eval test x\${$as_var+set} = xset \
-  && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
-done
-PS1='$ '
-PS2='> '
-PS4='+ '
-
-# NLS nuisances.
-LC_ALL=C
-export LC_ALL
-LANGUAGE=C
-export LANGUAGE
-
-# CDPATH.
-(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-
-
-# as_fn_error ERROR [LINENO LOG_FD]
-# ---------------------------------
-# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
-# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with status $?, using 1 if that was 0.
-as_fn_error ()
-{
-  as_status=$?; test $as_status -eq 0 && as_status=1
-  if test "$3"; then
-    as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-    $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3
-  fi
-  $as_echo "$as_me: error: $1" >&2
-  as_fn_exit $as_status
-} # as_fn_error
-
-
-# as_fn_set_status STATUS
-# -----------------------
-# Set $? to STATUS, without forking.
-as_fn_set_status ()
-{
-  return $1
-} # as_fn_set_status
-
-# as_fn_exit STATUS
-# -----------------
-# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
-as_fn_exit ()
-{
-  set +e
-  as_fn_set_status $1
-  exit $1
-} # as_fn_exit
-
-# as_fn_unset VAR
-# ---------------
-# Portably unset VAR.
-as_fn_unset ()
-{
-  { eval $1=; unset $1;}
-}
-as_unset=as_fn_unset
-# as_fn_append VAR VALUE
-# ----------------------
-# Append the text in VALUE to the end of the definition contained in VAR. Take
-# advantage of any shell optimizations that allow amortized linear growth over
-# repeated appends, instead of the typical quadratic growth present in naive
-# implementations.
-if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
-  eval 'as_fn_append ()
-  {
-    eval $1+=\$2
-  }'
-else
-  as_fn_append ()
-  {
-    eval $1=\$$1\$2
-  }
-fi # as_fn_append
-
-# as_fn_arith ARG...
-# ------------------
-# Perform arithmetic evaluation on the ARGs, and store the result in the
-# global $as_val. Take advantage of shells that can avoid forks. The arguments
-# must be portable across $(()) and expr.
-if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
-  eval 'as_fn_arith ()
-  {
-    as_val=$(( $* ))
-  }'
-else
-  as_fn_arith ()
-  {
-    as_val=`expr "$@" || test $? -eq 1`
-  }
-fi # as_fn_arith
-
-
-if expr a : '\(a\)' >/dev/null 2>&1 &&
-   test "X`expr 00001 : '.*\(...\)'`" = X001; then
-  as_expr=expr
-else
-  as_expr=false
-fi
-
-if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
-  as_basename=basename
-else
-  as_basename=false
-fi
-
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
-  as_dirname=dirname
-else
-  as_dirname=false
-fi
-
-as_me=`$as_basename -- "$0" ||
-$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
-	 X"$0" : 'X\(//\)$' \| \
-	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X/"$0" |
-    sed '/^.*\/\([^/][^/]*\)\/*$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\/\(\/\/\)$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\/\(\/\).*/{
-	    s//\1/
-	    q
-	  }
-	  s/.*/./; q'`
-
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
-
-ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in #(((((
--n*)
-  case `echo 'xy\c'` in
-  *c*) ECHO_T='	';;	# ECHO_T is single tab character.
-  xy)  ECHO_C='\c';;
-  *)   echo `echo ksh88 bug on AIX 6.1` > /dev/null
-       ECHO_T='	';;
-  esac;;
-*)
-  ECHO_N='-n';;
-esac
-
-rm -f conf$$ conf$$.exe conf$$.file
-if test -d conf$$.dir; then
-  rm -f conf$$.dir/conf$$.file
-else
-  rm -f conf$$.dir
-  mkdir conf$$.dir 2>/dev/null
-fi
-if (echo >conf$$.file) 2>/dev/null; then
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-    as_ln_s='ln -s'
-    # ... but there are two gotchas:
-    # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
-    # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
-    # In both cases, we have to default to `cp -p'.
-    ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
-      as_ln_s='cp -p'
-  elif ln conf$$.file conf$$ 2>/dev/null; then
-    as_ln_s=ln
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-    as_ln_s='cp -p'
-  fi
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-  as_ln_s='cp -p'
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-rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
-rmdir conf$$.dir 2>/dev/null
-
-
-# as_fn_mkdir_p
-# -------------
-# Create "$as_dir" as a directory, including parents if necessary.
-as_fn_mkdir_p ()
-{
-
-  case $as_dir in #(
-  -*) as_dir=./$as_dir;;
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-    as_dirs=
-    while :; do
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-      *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
-      *) as_qdir=$as_dir;;
-      esac
-      as_dirs="'$as_qdir' $as_dirs"
-      as_dir=`$as_dirname -- "$as_dir" ||
-$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-	 X"$as_dir" : 'X\(//\)[^/]' \| \
-	 X"$as_dir" : 'X\(//\)$' \| \
-	 X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$as_dir" |
-    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)[^/].*/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\).*/{
-	    s//\1/
-	    q
-	  }
-	  s/.*/./; q'`
-      test -d "$as_dir" && break
-    done
-    test -z "$as_dirs" || eval "mkdir $as_dirs"
-  } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
-
-
-} # as_fn_mkdir_p
-if mkdir -p . 2>/dev/null; then
-  as_mkdir_p='mkdir -p "$as_dir"'
-else
-  test -d ./-p && rmdir ./-p
-  as_mkdir_p=false
-fi
-
-if test -x / >/dev/null 2>&1; then
-  as_test_x='test -x'
-else
-  if ls -dL / >/dev/null 2>&1; then
-    as_ls_L_option=L
-  else
-    as_ls_L_option=
-  fi
-  as_test_x='
-    eval sh -c '\''
-      if test -d "$1"; then
-	test -d "$1/.";
-      else
-	case $1 in #(
-	-*)set "./$1";;
-	esac;
-	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
-	???[sx]*):;;*)false;;esac;fi
-    '\'' sh
-  '
-fi
-as_executable_p=$as_test_x
-
-# Sed expression to map a string onto a valid CPP name.
-as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
-
-# Sed expression to map a string onto a valid variable name.
-as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
-
-
-exec 6>&1
-## ----------------------------------- ##
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-  case $INSTALL in
-  [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
-  *) ac_INSTALL=$ac_top_build_prefix$INSTALL ;;
-  esac
-  ac_MKDIR_P=$MKDIR_P
-  case $MKDIR_P in
-  [\\/$]* | ?:[\\/]* ) ;;
-  */*) ac_MKDIR_P=$ac_top_build_prefix$MKDIR_P ;;
-  esac
-_ACEOF
-
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-# If the template does not know about datarootdir, expand it.
-# FIXME: This hack should be removed a few years after 2.60.
-ac_datarootdir_hack=; ac_datarootdir_seen=
-ac_sed_dataroot='
-/datarootdir/ {
-  p
-  q
-}
-/@datadir@/p
-/@docdir@/p
-/@infodir@/p
-/@localedir@/p
-/@mandir@/p'
-case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
-*datarootdir*) ac_datarootdir_seen=yes;;
-*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
-$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
-_ACEOF
-cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-  ac_datarootdir_hack='
-  s&@datadir@&$datadir&g
-  s&@docdir@&$docdir&g
-  s&@infodir@&$infodir&g
-  s&@localedir@&$localedir&g
-  s&@mandir@&$mandir&g
-  s&\\\${datarootdir}&$datarootdir&g' ;;
-esac
-_ACEOF
-
-# Neutralize VPATH when `$srcdir' = `.'.
-# Shell code in configure.ac might set extrasub.
-# FIXME: do we really want to maintain this feature?
-cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-ac_sed_extra="$ac_vpsub
-$extrasub
-_ACEOF
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-:t
-/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
-s|@configure_input@|$ac_sed_conf_input|;t t
-s&@top_builddir@&$ac_top_builddir_sub&;t t
-s&@top_build_prefix@&$ac_top_build_prefix&;t t
-s&@srcdir@&$ac_srcdir&;t t
-s&@abs_srcdir@&$ac_abs_srcdir&;t t
-s&@top_srcdir@&$ac_top_srcdir&;t t
-s&@abs_top_srcdir@&$ac_abs_top_srcdir&;t t
-s&@builddir@&$ac_builddir&;t t
-s&@abs_builddir@&$ac_abs_builddir&;t t
-s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
-s&@INSTALL@&$ac_INSTALL&;t t
-s&@MKDIR_P@&$ac_MKDIR_P&;t t
-$ac_datarootdir_hack
-"
-eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
-  || as_fn_error "could not create $ac_file" "$LINENO" 5
-
-test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
-  { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
-  { ac_out=`sed -n '/^[	 ]*datarootdir[	 ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined.  Please make sure it is defined." >&5
-$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
-which seems to be undefined.  Please make sure it is defined." >&2;}
-
-  rm -f "$tmp/stdin"
-  case $ac_file in
-  -) cat "$tmp/out" && rm -f "$tmp/out";;
-  *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
-  esac \
-  || as_fn_error "could not create $ac_file" "$LINENO" 5
- ;;
-  :H)
-  #
-  # CONFIG_HEADER
-  #
-  if test x"$ac_file" != x-; then
-    {
-      $as_echo "/* $configure_input  */" \
-      && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
-    } >"$tmp/config.h" \
-      || as_fn_error "could not create $ac_file" "$LINENO" 5
-    if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
-      { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
-$as_echo "$as_me: $ac_file is unchanged" >&6;}
-    else
-      rm -f "$ac_file"
-      mv "$tmp/config.h" "$ac_file" \
-	|| as_fn_error "could not create $ac_file" "$LINENO" 5
-    fi
-  else
-    $as_echo "/* $configure_input  */" \
-      && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
-      || as_fn_error "could not create -" "$LINENO" 5
-  fi
-# Compute "$ac_file"'s index in $config_headers.
-_am_arg="$ac_file"
-_am_stamp_count=1
-for _am_header in $config_headers :; do
-  case $_am_header in
-    $_am_arg | $_am_arg:* )
-      break ;;
-    * )
-      _am_stamp_count=`expr $_am_stamp_count + 1` ;;
-  esac
-done
-echo "timestamp for $_am_arg" >`$as_dirname -- "$_am_arg" ||
-$as_expr X"$_am_arg" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-	 X"$_am_arg" : 'X\(//\)[^/]' \| \
-	 X"$_am_arg" : 'X\(//\)$' \| \
-	 X"$_am_arg" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$_am_arg" |
-    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)[^/].*/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\).*/{
-	    s//\1/
-	    q
-	  }
-	  s/.*/./; q'`/stamp-h$_am_stamp_count
- ;;
-
-  :C)  { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
-$as_echo "$as_me: executing $ac_file commands" >&6;}
- ;;
-  esac
-
-
-  case $ac_file$ac_mode in
-    "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
-  # Autoconf 2.62 quotes --file arguments for eval, but not when files
-  # are listed without --file.  Let's play safe and only enable the eval
-  # if we detect the quoting.
-  case $CONFIG_FILES in
-  *\'*) eval set x "$CONFIG_FILES" ;;
-  *)   set x $CONFIG_FILES ;;
-  esac
-  shift
-  for mf
-  do
-    # Strip MF so we end up with the name of the file.
-    mf=`echo "$mf" | sed -e 's/:.*$//'`
-    # Check whether this is an Automake generated Makefile or not.
-    # We used to match only the files named `Makefile.in', but
-    # some people rename them; so instead we look at the file content.
-    # Grep'ing the first line is not enough: some people post-process
-    # each Makefile.in and add a new line on top of each file to say so.
-    # Grep'ing the whole file is not good either: AIX grep has a line
-    # limit of 2048, but all sed's we know have understand at least 4000.
-    if sed -n 's,^#.*generated by automake.*,X,p' "$mf" | grep X >/dev/null 2>&1; then
-      dirpart=`$as_dirname -- "$mf" ||
-$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-	 X"$mf" : 'X\(//\)[^/]' \| \
-	 X"$mf" : 'X\(//\)$' \| \
-	 X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$mf" |
-    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)[^/].*/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\).*/{
-	    s//\1/
-	    q
-	  }
-	  s/.*/./; q'`
-    else
-      continue
-    fi
-    # Extract the definition of DEPDIR, am__include, and am__quote
-    # from the Makefile without running `make'.
-    DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
-    test -z "$DEPDIR" && continue
-    am__include=`sed -n 's/^am__include = //p' < "$mf"`
-    test -z "am__include" && continue
-    am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
-    # When using ansi2knr, U may be empty or an underscore; expand it
-    U=`sed -n 's/^U = //p' < "$mf"`
-    # Find all dependency output files, they are included files with
-    # $(DEPDIR) in their names.  We invoke sed twice because it is the
-    # simplest approach to changing $(DEPDIR) to its actual value in the
-    # expansion.
-    for file in `sed -n "
-      s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
-	 sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
-      # Make sure the directory exists.
-      test -f "$dirpart/$file" && continue
-      fdir=`$as_dirname -- "$file" ||
-$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
-	 X"$file" : 'X\(//\)[^/]' \| \
-	 X"$file" : 'X\(//\)$' \| \
-	 X"$file" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$file" |
-    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)[^/].*/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\/\)$/{
-	    s//\1/
-	    q
-	  }
-	  /^X\(\/\).*/{
-	    s//\1/
-	    q
-	  }
-	  s/.*/./; q'`
-      as_dir=$dirpart/$fdir; as_fn_mkdir_p
-      # echo "creating $dirpart/$file"
-      echo '# dummy' > "$dirpart/$file"
-    done
-  done
-}
- ;;
-
-  esac
-done # for ac_tag
-
-
-as_fn_exit 0
-_ACEOF
-ac_clean_files=$ac_clean_files_save
-
-test $ac_write_fail = 0 ||
-  as_fn_error "write failure creating $CONFIG_STATUS" "$LINENO" 5
-
-
-# configure is writing to config.log, and then calls config.status.
-# config.status does its own redirection, appending to config.log.
-# Unfortunately, on DOS this fails, as config.log is still kept open
-# by configure, so config.status won't be able to write to it; its
-# output is simply discarded.  So we exec the FD to /dev/null,
-# effectively closing config.log, so it can be properly (re)opened and
-# appended to by config.status.  When coming back to configure, we
-# need to make the FD available again.
-if test "$no_create" != yes; then
-  ac_cs_success=:
-  ac_config_status_args=
-  test "$silent" = yes &&
-    ac_config_status_args="$ac_config_status_args --quiet"
-  exec 5>/dev/null
-  $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
-  exec 5>>config.log
-  # Use ||, not &&, to avoid exiting from the if with $? = 1, which
-  # would make configure fail if this is the last instruction.
-  $ac_cs_success || as_fn_exit $?
-fi
-if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
-$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
-fi
-
-ac_config_files="$ac_config_files doc/examples/Makefile"
+ac_config_files="$ac_config_files scripts/Makefile doc/examples/Makefile lib/Makefile"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -8441,10 +6955,6 @@ if test -z "${HAVE_CAIRO_TRUE}" && test -z "${HAVE_CAIRO_FALSE}"; then
   as_fn_error "conditional \"HAVE_CAIRO\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5
 fi
-if test -z "${am__EXEEXT_TRUE}" && test -z "${am__EXEEXT_FALSE}"; then
-  as_fn_error "conditional \"am__EXEEXT\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
 
 : ${CONFIG_STATUS=./config.status}
 ac_write_fail=0
@@ -9043,7 +7553,6 @@ for ac_config_target in $ac_config_targets
 do
   case $ac_config_target in
     "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
-    "lib/Makefile") CONFIG_FILES="$CONFIG_FILES lib/Makefile" ;;
     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
     "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
@@ -9051,6 +7560,7 @@ do
     "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;;
   esac
diff --git a/configure.ac b/configure.ac
index 7308b984..2a58233a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -7,8 +7,6 @@ VERSION=AC_PACKAGE_VERSION
 AM_CONFIG_HEADER(config.h)
 AM_INIT_AUTOMAKE(crystfel, "$VERSION")
 
-AC_CONFIG_FILES(lib/Makefile)
-
 AC_PROG_CC
 gl_EARLY
 AC_PROG_AWK
@@ -148,5 +146,6 @@ 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_OUTPUT(Makefile src/Makefile data/Makefile doc/Makefile scripts/Makefile)
-AC_OUTPUT(doc/examples/Makefile)
+AC_CONFIG_FILES(Makefile src/Makefile data/Makefile doc/Makefile)
+AC_CONFIG_FILES(scripts/Makefile doc/examples/Makefile lib/Makefile)
+AC_OUTPUT
diff --git a/src/Makefile.in b/src/Makefile.in
index 5c2d7627..370ca3da 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -119,17 +119,17 @@ hdfsee_OBJECTS = $(am_hdfsee_OBJECTS)
 hdfsee_DEPENDENCIES =
 am__indexamajig_SOURCES_DIST = indexamajig.c hdf5-file.c utils.c \
 	cell.c image.c peaks.c index.c filters.c diffraction.c \
-	detector.c sfac.c dirax.c reflections.c templates.c symmetry.c \
-	geometry.c thread-pool.c beam-parameters.c diffraction-gpu.c \
-	cl-utils.c
+	detector.c sfac.c dirax.c mosflm.c reflections.c templates.c \
+	symmetry.c geometry.c thread-pool.c beam-parameters.c \
+	diffraction-gpu.c cl-utils.c
 @HAVE_OPENCL_TRUE@am__objects_1 = diffraction-gpu.$(OBJEXT) \
 @HAVE_OPENCL_TRUE@	cl-utils.$(OBJEXT)
 am_indexamajig_OBJECTS = indexamajig.$(OBJEXT) hdf5-file.$(OBJEXT) \
 	utils.$(OBJEXT) cell.$(OBJEXT) image.$(OBJEXT) peaks.$(OBJEXT) \
 	index.$(OBJEXT) filters.$(OBJEXT) diffraction.$(OBJEXT) \
 	detector.$(OBJEXT) sfac.$(OBJEXT) dirax.$(OBJEXT) \
-	reflections.$(OBJEXT) templates.$(OBJEXT) symmetry.$(OBJEXT) \
-	geometry.$(OBJEXT) thread-pool.$(OBJEXT) \
+	mosflm.$(OBJEXT) reflections.$(OBJEXT) templates.$(OBJEXT) \
+	symmetry.$(OBJEXT) geometry.$(OBJEXT) thread-pool.$(OBJEXT) \
 	beam-parameters.$(OBJEXT) $(am__objects_1)
 indexamajig_OBJECTS = $(am_indexamajig_OBJECTS)
 indexamajig_DEPENDENCIES =
@@ -158,8 +158,9 @@ process_hkl_DEPENDENCIES =
 am_reintegrate_OBJECTS = reintegrate.$(OBJEXT) cell.$(OBJEXT) \
 	hdf5-file.$(OBJEXT) utils.$(OBJEXT) detector.$(OBJEXT) \
 	peaks.$(OBJEXT) image.$(OBJEXT) stream.$(OBJEXT) \
-	index.$(OBJEXT) dirax.$(OBJEXT) templates.$(OBJEXT) \
-	geometry.$(OBJEXT) symmetry.$(OBJEXT) thread-pool.$(OBJEXT)
+	index.$(OBJEXT) dirax.$(OBJEXT) mosflm.$(OBJEXT) \
+	templates.$(OBJEXT) geometry.$(OBJEXT) symmetry.$(OBJEXT) \
+	thread-pool.$(OBJEXT)
 reintegrate_OBJECTS = $(am_reintegrate_OBJECTS)
 reintegrate_DEPENDENCIES =
 am_render_hkl_OBJECTS = render_hkl.$(OBJEXT) cell.$(OBJEXT) \
@@ -409,8 +410,8 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
 process_hkl_LDADD = @LIBS@
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
 	peaks.c index.c filters.c diffraction.c detector.c sfac.c \
-	dirax.c reflections.c templates.c symmetry.c geometry.c \
-	thread-pool.c beam-parameters.c $(am__append_3)
+	dirax.c mosflm.c reflections.c templates.c symmetry.c \
+	geometry.c thread-pool.c beam-parameters.c $(am__append_3)
 indexamajig_LDADD = @LIBS@
 @HAVE_GTK_TRUE@hdfsee_SOURCES = hdfsee.c displaywindow.c render.c hdf5-file.c utils.c image.c \
 @HAVE_GTK_TRUE@                 filters.c
@@ -451,8 +452,8 @@ facetron_LDADD = @LIBS@
 @HAVE_CAIRO_TRUE@cubeit_LDADD = @LIBS@
 reintegrate_SOURCES = reintegrate.c cell.c hdf5-file.c utils.c detector.c \
                       peaks.c image.c stream.c \
-                      index.c dirax.c templates.c geometry.c symmetry.c \
-                      thread-pool.c
+                      index.c dirax.c mosflm.c templates.c geometry.c \
+                      symmetry.c thread-pool.c
 
 reintegrate_LDADD = @LIBS@
 estimate_background_SOURCES = estimate_background.c stream.c utils.c cell.c
@@ -460,7 +461,7 @@ estimate_background_LDADD = @LIBS@
 INCLUDES = "-I$(top_srcdir)/data"
 EXTRA_DIST = cell.h hdf5-file.h image.h  utils.h diffraction.h detector.h \
              sfac.h reflections.h list_tmp.h statistics.h displaywindow.h \
-             render.h hdfsee.h dirax.h peaks.h index.h  filters.h \
+             render.h hdfsee.h dirax.h mosflm.h peaks.h index.h  filters.h \
              diffraction-gpu.h cl-utils.h symmetry.h \
              povray.h index-priv.h geometry.h templates.h render_hkl.h \
              stream.h thread-pool.h beam-parameters.h post-refinement.h \
@@ -609,6 +610,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/image.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/index.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/indexamajig.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mosflm.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pattern_sim.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/peaks.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/post-refinement.Po@am__quote@
diff --git a/src/cell.c b/src/cell.c
index fa3cfb0a..4c6a4ed7 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -887,7 +887,7 @@ UnitCell *load_cell_from_pdb(const char *filename)
 				notrail(sym);
 				cell_set_pointgroup_from_pdb(cell, sym);
 				cell->spacegroup = sym;
-				
+
 			} else {
 				cell_set_pointgroup_from_pdb(cell, "P 1");
 				cell->spacegroup = strdup("P 1");