Index: Makefile.in
===================================================================
--- Makefile.in	(revision 8a0a7309bf86e67ae52fb58ccd98510394b9e722)
+++ Makefile.in	(revision 6aa5ec0f028f7e04c66c00bd48ae64b4cb942f7d)
@@ -146,4 +146,5 @@
 LIBS = @LIBS@
 LTLIBOBJS = @LTLIBOBJS@
+MAINT = @MAINT@
 MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
@@ -215,5 +216,5 @@
 am--refresh: Makefile
 	@:
-$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__configure_deps)
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
@@ -242,7 +243,7 @@
 	$(SHELL) ./config.status --recheck
 
-$(top_srcdir)/configure:  $(am__configure_deps)
+$(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 	$(am__cd) $(srcdir) && $(AUTOCONF)
-$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+$(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
 $(am__aclocal_m4_deps):
@@ -255,5 +256,5 @@
 	@rm -f stamp-h1
 	cd $(top_builddir) && $(SHELL) ./config.status config.h
-$(srcdir)/config.h.in:  $(am__configure_deps) 
+$(srcdir)/config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps) 
 	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
 	rm -f stamp-h1
Index: aclocal.m4
===================================================================
--- aclocal.m4	(revision 8a0a7309bf86e67ae52fb58ccd98510394b9e722)
+++ aclocal.m4	(revision 6aa5ec0f028f7e04c66c00bd48ae64b4cb942f7d)
@@ -601,4 +601,44 @@
 AC_SUBST([am__leading_dot])])
 
+# Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-
+# From Jim Meyering
+
+# Copyright (C) 1996, 1998, 2000, 2001, 2002, 2003, 2004, 2005, 2008,
+# 2011 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 5
+
+# AM_MAINTAINER_MODE([DEFAULT-MODE])
+# ----------------------------------
+# Control maintainer-specific portions of Makefiles.
+# Default is to disable them, unless `enable' is passed literally.
+# For symmetry, `disable' may be passed as well.  Anyway, the user
+# can override the default with the --enable/--disable switch.
+AC_DEFUN([AM_MAINTAINER_MODE],
+[m4_case(m4_default([$1], [disable]),
+       [enable], [m4_define([am_maintainer_other], [disable])],
+       [disable], [m4_define([am_maintainer_other], [enable])],
+       [m4_define([am_maintainer_other], [enable])
+        m4_warn([syntax], [unexpected argument to AM@&t@_MAINTAINER_MODE: $1])])
+AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])
+  dnl maintainer-mode's default is 'disable' unless 'enable' is passed
+  AC_ARG_ENABLE([maintainer-mode],
+[  --][am_maintainer_other][-maintainer-mode  am_maintainer_other make rules and dependencies not useful
+			  (and sometimes confusing) to the casual installer],
+      [USE_MAINTAINER_MODE=$enableval],
+      [USE_MAINTAINER_MODE=]m4_if(am_maintainer_other, [enable], [no], [yes]))
+  AC_MSG_RESULT([$USE_MAINTAINER_MODE])
+  AM_CONDITIONAL([MAINTAINER_MODE], [test $USE_MAINTAINER_MODE = yes])
+  MAINT=$MAINTAINER_MODE_TRUE
+  AC_SUBST([MAINT])dnl
+]
+)
+
+AU_DEFUN([jm_MAINTAINER_MODE], [AM_MAINTAINER_MODE])
+
 # Check to see how 'make' treats includes.	            -*- Autoconf -*-
 
Index: configure
===================================================================
--- configure	(revision 8a0a7309bf86e67ae52fb58ccd98510394b9e722)
+++ configure	(revision 6aa5ec0f028f7e04c66c00bd48ae64b4cb942f7d)
@@ -640,4 +640,7 @@
 BACKEND_CC
 GCC_PATH
+MAINT
+MAINTAINER_MODE_FALSE
+MAINTAINER_MODE_TRUE
 am__untar
 am__tar
@@ -704,4 +707,5 @@
 ac_user_opts='
 enable_option_checking
+enable_maintainer_mode
 with_backend_compiler
 enable_dependency_tracking
@@ -1335,4 +1339,6 @@
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
+  --enable-maintainer-mode  enable make rules and dependencies not useful
+			  (and sometimes confusing) to the casual installer
   --disable-dependency-tracking  speeds up one-time build
   --enable-dependency-tracking   do not reject slow dependency extractors
@@ -2866,4 +2872,27 @@
 
 
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to enable maintainer-specific portions of Makefiles" >&5
+$as_echo_n "checking whether to enable maintainer-specific portions of Makefiles... " >&6; }
+    # Check whether --enable-maintainer-mode was given.
+if test "${enable_maintainer_mode+set}" = set; then :
+  enableval=$enable_maintainer_mode; USE_MAINTAINER_MODE=$enableval
+else
+  USE_MAINTAINER_MODE=no
+fi
+
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $USE_MAINTAINER_MODE" >&5
+$as_echo "$USE_MAINTAINER_MODE" >&6; }
+   if test $USE_MAINTAINER_MODE = yes; then
+  MAINTAINER_MODE_TRUE=
+  MAINTAINER_MODE_FALSE='#'
+else
+  MAINTAINER_MODE_TRUE='#'
+  MAINTAINER_MODE_FALSE=
+fi
+
+  MAINT=$MAINTAINER_MODE_TRUE
+
+
+
 ac_config_headers="$ac_config_headers config.h"
 
@@ -5453,4 +5482,8 @@
 fi
 
+if test -z "${MAINTAINER_MODE_TRUE}" && test -z "${MAINTAINER_MODE_FALSE}"; then
+  as_fn_error $? "conditional \"MAINTAINER_MODE\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
 if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
   as_fn_error $? "conditional \"AMDEP\" was never defined.
Index: configure.ac
===================================================================
--- configure.ac	(revision 8a0a7309bf86e67ae52fb58ccd98510394b9e722)
+++ configure.ac	(revision 6aa5ec0f028f7e04c66c00bd48ae64b4cb942f7d)
@@ -4,6 +4,6 @@
 AC_PREREQ([2.68])
 AC_INIT([cfa-cc],[1.0.0],[cforall@plg.uwaterloo.ca])
-#AM_INIT_AUTOMAKE([foreign])		# do not follow GNU standard
 AM_INIT_AUTOMAKE
+AM_MAINTAINER_MODE(disable)
 AC_CONFIG_SRCDIR([src/main.cc])
 AC_CONFIG_HEADERS([config.h])
Index: missing
===================================================================
--- missing	(revision 8a0a7309bf86e67ae52fb58ccd98510394b9e722)
+++ missing	(revision 6aa5ec0f028f7e04c66c00bd48ae64b4cb942f7d)
@@ -1,1 +1,331 @@
-exit 0	# aclocal.m4 is included, and hence, does not need to be remade, especial when git does not preserve file timestamps
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2012-01-06.13; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009, 2010, 2011, 2012 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
+
+# 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.
+
+if test $# -eq 0; then
+  echo 1>&2 "Try \`$0 --help' for more information"
+  exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+  configure_ac=configure.ac
+else
+  configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+  # Try to run requested program, and just exit if it succeeds.
+  run=
+  shift
+  "$@" && exit 0
+  # Exit code 63 means version mismatch.  This often happens
+  # when the user try to use an ancient version of a tool on
+  # a file that requires a minimum version.  In this case we
+  # we should proceed has if the program had been absent, or
+  # if --run hadn't been passed.
+  if test $? = 63; then
+    run=:
+    msg="probably too old"
+  fi
+  ;;
+
+  -h|--h|--he|--hel|--help)
+    echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+  -h, --help      display this help and exit
+  -v, --version   output version information and exit
+  --run           try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+  aclocal      touch file \`aclocal.m4'
+  autoconf     touch file \`configure'
+  autoheader   touch file \`config.h.in'
+  autom4te     touch the output file, or create a stub one
+  automake     touch all \`Makefile.in' files
+  bison        create \`y.tab.[ch]', if possible, from existing .[ch]
+  flex         create \`lex.yy.c', if possible, from existing .c
+  help2man     touch the output file
+  lex          create \`lex.yy.c', if possible, from existing .c
+  makeinfo     touch the output file
+  yacc         create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
+Send bug reports to <bug-automake@gnu.org>."
+    exit $?
+    ;;
+
+  -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+    echo "missing $scriptversion (GNU Automake)"
+    exit $?
+    ;;
+
+  -*)
+    echo 1>&2 "$0: Unknown \`$1' option"
+    echo 1>&2 "Try \`$0 --help' for more information"
+    exit 1
+    ;;
+
+esac
+
+# normalize program name to check for.
+program=`echo "$1" | sed '
+  s/^gnu-//; t
+  s/^gnu//; t
+  s/^g//; t'`
+
+# Now exit if we have it, but it failed.  Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program).  This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+  lex*|yacc*)
+    # Not GNU programs, they don't have --version.
+    ;;
+
+  *)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+       # Could not run --version or --help.  This is probably someone
+       # running `$TOOL --version' or `$TOOL --help' to check whether
+       # $TOOL exists and not knowing $TOOL uses missing.
+       exit 1
+    fi
+    ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+  aclocal*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`acinclude.m4' or \`${configure_ac}'.  You might want
+         to install the \`Automake' and \`Perl' packages.  Grab them from
+         any GNU archive site."
+    touch aclocal.m4
+    ;;
+
+  autoconf*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`${configure_ac}'.  You might want to install the
+         \`Autoconf' and \`GNU m4' packages.  Grab them from any GNU
+         archive site."
+    touch configure
+    ;;
+
+  autoheader*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`acconfig.h' or \`${configure_ac}'.  You might want
+         to install the \`Autoconf' and \`GNU m4' packages.  Grab them
+         from any GNU archive site."
+    files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+    test -z "$files" && files="config.h"
+    touch_files=
+    for f in $files; do
+      case $f in
+      *:*) touch_files="$touch_files "`echo "$f" |
+				       sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+      *) touch_files="$touch_files $f.in";;
+      esac
+    done
+    touch $touch_files
+    ;;
+
+  automake*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+         You might want to install the \`Automake' and \`Perl' packages.
+         Grab them from any GNU archive site."
+    find . -type f -name Makefile.am -print |
+	   sed 's/\.am$/.in/' |
+	   while read f; do touch "$f"; done
+    ;;
+
+  autom4te*)
+    echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+         You might have modified some files without having the
+         proper tools for further handling them.
+         You can get \`$1' as part of \`Autoconf' from any GNU
+         archive site."
+
+    file=`echo "$*" | sed -n "$sed_output"`
+    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+    if test -f "$file"; then
+	touch $file
+    else
+	test -z "$file" || exec >$file
+	echo "#! /bin/sh"
+	echo "# Created by GNU Automake missing as a replacement of"
+	echo "#  $ $@"
+	echo "exit 0"
+	chmod +x $file
+	exit 1
+    fi
+    ;;
+
+  bison*|yacc*)
+    echo 1>&2 "\
+WARNING: \`$1' $msg.  You should only need it if
+         you modified a \`.y' file.  You may need the \`Bison' package
+         in order for those modifications to take effect.  You can get
+         \`Bison' from any GNU archive site."
+    rm -f y.tab.c y.tab.h
+    if test $# -ne 1; then
+        eval LASTARG=\${$#}
+	case $LASTARG in
+	*.y)
+	    SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+	    if test -f "$SRCFILE"; then
+	         cp "$SRCFILE" y.tab.c
+	    fi
+	    SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+	    if test -f "$SRCFILE"; then
+	         cp "$SRCFILE" y.tab.h
+	    fi
+	  ;;
+	esac
+    fi
+    if test ! -f y.tab.h; then
+	echo >y.tab.h
+    fi
+    if test ! -f y.tab.c; then
+	echo 'main() { return 0; }' >y.tab.c
+    fi
+    ;;
+
+  lex*|flex*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified a \`.l' file.  You may need the \`Flex' package
+         in order for those modifications to take effect.  You can get
+         \`Flex' from any GNU archive site."
+    rm -f lex.yy.c
+    if test $# -ne 1; then
+        eval LASTARG=\${$#}
+	case $LASTARG in
+	*.l)
+	    SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+	    if test -f "$SRCFILE"; then
+	         cp "$SRCFILE" lex.yy.c
+	    fi
+	  ;;
+	esac
+    fi
+    if test ! -f lex.yy.c; then
+	echo 'main() { return 0; }' >lex.yy.c
+    fi
+    ;;
+
+  help2man*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+	 you modified a dependency of a manual page.  You may need the
+	 \`Help2man' package in order for those modifications to take
+	 effect.  You can get \`Help2man' from any GNU archive site."
+
+    file=`echo "$*" | sed -n "$sed_output"`
+    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+    if test -f "$file"; then
+	touch $file
+    else
+	test -z "$file" || exec >$file
+	echo ".ab help2man is required to generate this page"
+	exit $?
+    fi
+    ;;
+
+  makeinfo*)
+    echo 1>&2 "\
+WARNING: \`$1' is $msg.  You should only need it if
+         you modified a \`.texi' or \`.texinfo' file, or any other file
+         indirectly affecting the aspect of the manual.  The spurious
+         call might also be the consequence of using a buggy \`make' (AIX,
+         DU, IRIX).  You might want to install the \`Texinfo' package or
+         the \`GNU make' package.  Grab either from any GNU archive site."
+    # The file to touch is that specified with -o ...
+    file=`echo "$*" | sed -n "$sed_output"`
+    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+    if test -z "$file"; then
+      # ... or it is the one specified with @setfilename ...
+      infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+      file=`sed -n '
+	/^@setfilename/{
+	  s/.* \([^ ]*\) *$/\1/
+	  p
+	  q
+	}' $infile`
+      # ... or it is derived from the source name (dir/f.texi becomes f.info)
+      test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+    fi
+    # If the file does not exist, the user really needs makeinfo;
+    # let's fail without touching anything.
+    test -f $file || exit 1
+    touch $file
+    ;;
+
+  *)
+    echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+         You might have modified some files without having the
+         proper tools for further handling them.  Check the \`README' file,
+         it often tells you about the needed prerequisites for installing
+         this package.  You may also peek at any GNU archive site, in case
+         some other package would contain this missing \`$1' program."
+    exit 1
+    ;;
+esac
+
+exit 0
+
+# Local variables:
+# 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: