latexdiff

git-svn-id: svn://tug.org/texlive/trunk@34824 c570f23f-e606-0410-a88d-b1316a301751

10 files changed, 815 insertions, 170 deletions

diff --git a/Master/texmf-dist/doc/support/latexdiff/Makefile b/Master/texmf-dist/doc/support/latexdiff/Makefile
new file mode 100644
index 00000000000..45467307879
--- /dev/null
+++ b/Master/texmf-dist/doc/support/latexdiff/Makefile
@@ -0,0 +1,64 @@
+# Modify these paths to the requirements of your own system
+# For the current setting you will need root permission but 
+# it is perfectly acceptable to choose user directories 
+#
+INSTALLPATH = /usr/local
+INSTALLMANPATH = $(INSTALLPATH)/man
+INSTALLEXECPATH = $(INSTALLPATH)/bin
+
+default:
+	@echo "To install stand-alone version type:    make install"
+	@echo "  (Note the standard version requires prior installation"
+	@echo "   of the PERL package Algorithm::Diff available from "
+	@echo "   the PERL archive www.cpan.org)"
+	@echo " "
+	@echo "To install fast version (using UNIX diff) type: make install fast "
+	@echo " "
+	@echo "To install the version which uses the system Algorithm::Diff package type: make install-ext"
+	@echo " "
+
+install: install-so
+
+install-ext: install-latexdiff install-latexrevise install-latexdiff-vc install-man
+
+install-so: install-latexdiff-so install-latexrevise install-latexdiff-vc install-man
+
+install-fast: install-latexdiff-fast install-latexrevise install-latexdiff-vc install-man
+
+install-man:
+	install latexrevise.1 latexdiff.1 latexdiff-vc.1 $(INSTALLMANPATH)/man1
+
+install-latexdiff:
+	install latexdiff $(INSTALLEXECPATH)
+
+install-latexdiff-so:
+	if [ -e $(INSTALLEXECPATH)/latexdiff ]; then rm $(INSTALLEXECPATH)/latexdiff; fi
+	install latexdiff-so $(INSTALLEXECPATH)
+	cd $(INSTALLEXECPATH); ln -s latexdiff-so latexdiff
+
+install-latexdiff-fast:
+	if [ -e $(INSTALLEXECPATH)/latexdiff ]; then rm $(INSTALLEXECPATH)/latexdiff; fi
+	install latexdiff-fast $(INSTALLEXECPATH)
+	cd $(INSTALLEXECPATH); ln -s latexdiff-fast latexdiff
+
+install-latexrevise:
+	install latexrevise $(INSTALLEXECPATH)
+
+install-latexdiff-vc:
+	install latexdiff-vc $(INSTALLEXECPATH)
+	cd $(INSTALLEXECPATH); for vcs in cvs rcs svn ; do if [ -e latexdiff-$$vcs ]; then rm latexdiff-$$vcs; fi; ln -s latexdiff-vc latexdiff-$$vcs ; done
+
+test-ext: 
+	@echo "latexdiff example/example-draft.tex example/example-rev.tex (system Algorithm::Diff)"
+	./latexdiff -V example/example-draft.tex example/example-rev.tex > example/example-diff.tex
+	@echo "Difference file created: example/example-diff.tex"
+
+test-so: 
+	@echo "latexdiff example/example-draft.tex example/example-rev.tex (stand-alone version)"
+	./latexdiff-so -V example/example-draft.tex example/example-rev.tex > example/example-diff.tex
+	@echo "Difference file created: example/example-diff.tex"
+
+test-fast: 
+	@echo "latexdiff example/example-draft.tex example/example-rev.tex (stand-alone version)"
+	./latexdiff-fast -V example/example-draft.tex example/example-rev.tex > example/example-diff.tex
+	@echo "Difference file created: example/example-diff.tex"
diff --git a/Master/texmf-dist/doc/support/latexdiff/README b/Master/texmf-dist/doc/support/latexdiff/README
index 7c7ff86766b..e9e189350e0 100644
--- a/Master/texmf-dist/doc/support/latexdiff/README
+++ b/Master/texmf-dist/doc/support/latexdiff/README
@@ -48,7 +48,7 @@ The basic installation procedure is almost trivial:
 3. Optionally create soft links latexdiff-cvs latexdiff-rcs, and
    latexdiff-svn for latexdiff-vc.
 
-The attached Makefile contains example commands to carry out above 
+The attached trivial Makefile contains example commands to carry out above 
 steps as root for a typical UNIX installation. Type 
 
   make install          (for the stand alone version)
@@ -65,7 +65,8 @@ or
 or
   make test-fast
 
-to test the respective versions on a brief example before installation
+to test the respective versions on a brief example before installation. It will often be
+as easy to carry out these steps manually instead of using the Makefile.
 
 
 DOCUMENTATION:
diff --git a/Master/texmf-dist/doc/support/latexdiff/contrib/README.latexchanges b/Master/texmf-dist/doc/support/latexdiff/contrib/README.latexchanges
new file mode 100644
index 00000000000..4a027658444
--- /dev/null
+++ b/Master/texmf-dist/doc/support/latexdiff/contrib/README.latexchanges
@@ -0,0 +1,13 @@
+latexchanges.py (Jan-Ake Larsson):
+Here's a wrapper I wrote for latexdiff, intended as a drop-in
+replacement for latex, when you have several numbered (or dated)
+versions of a manuscript. My coauthors don't as a rule know what CVS or
+SVN is, they simply use a number or date for the different versions.
+
+latexchanges replaces the current DVI with one that includes a
+latexdiff to the last version. The last version is selected as the
+TEX file in the same directory with the same prefix (up to a number
+or a dot), that has an mtime immediately preceding the given TEX
+file.
+
+
diff --git a/Master/texmf-dist/doc/support/latexdiff/contrib/latexchanges.py b/Master/texmf-dist/doc/support/latexdiff/contrib/latexchanges.py
new file mode 100644
index 00000000000..de7acbe8258
--- /dev/null
+++ b/Master/texmf-dist/doc/support/latexdiff/contrib/latexchanges.py
@@ -0,0 +1,67 @@
+#! /bin/env python
+# latexchanges
+#
+# Wrapper for latexdiff, intended as a drop-in replacement for latex,
+# when you have several numbered (or dated) versions of a manuscript.
+# My coauthors don't as a rule know what CVS or SVN is, they simply
+# use a number or date for the different versions.
+#
+# latexchanges replaces the current DVI with one that includes a
+# latexdiff to the last version. The last version is selected as the
+# TEX file in the same directory with the same prefix (up to a number
+# or a dot), that has an mtime immediately preceding the given TEX
+# file.
+#
+# (I should probably add CVS version numbering too, at some point.)
+#
+# Copyright (C) 2009 by Jan-\AA{}ke Larsson <jan-ake.larsson@liu.se>
+# Released under the terms of the GNU General Public License (GPL)
+# Version 2.  See http://www.gnu.org/ for details.
+#
+# Please do provide patches and bug reports, but remember: if it
+# breaks, you get to keep the pieces.
+#
+# Jan-\AA{}ke Larsson
+# Sept 16 2009
+
+from os import listdir,system,stat
+from sys import argv
+from re import split
+
+name=""
+newarg=[]
+
+# Find filename argument
+for i in range(1,len(argv)):
+    if argv[i][-4:]==".tex":
+        basename=split('[0-9.]',argv[i])[0]
+        name=argv[i][:-4]
+        newarg.append(name+".changes.tex")
+    else:
+        newarg.append(argv[i])
+
+if name:
+    print "Filename",name+".tex"
+    print "Prefix is",basename
+    # Find last archived version
+    mtime=stat(name+".tex").st_mtime
+    old_mtime=0
+    ls=listdir(".")
+    for j in ls:
+        if j.startswith(basename) and j.endswith(".tex")\
+               and not j.endswith(".changes.tex"):
+            tmptime=stat(j).st_mtime
+            if mtime>tmptime and old_mtime<tmptime:
+                oldname=j
+                old_mtime=tmptime
+
+    # Archived version found?
+    if old_mtime>0:
+        print "Comparing with",oldname
+        system ("/bin/cp "+name+".aux "+name+".changes.aux")
+        system ("/bin/cp "+name+".bbl "+name+".changes.bbl")
+        system ("latexdiff "+oldname+" "+name+".tex > "+name+".changes.tex")
+        system ("latex "+" ".join(newarg))
+        system ("cp "+name+".changes.dvi "+name+".dvi")
+    else:
+        system ("latex "+" ".join(argv[1:]))
diff --git a/Master/texmf-dist/doc/support/latexdiff/contrib/latexdiff-wrap b/Master/texmf-dist/doc/support/latexdiff/contrib/latexdiff-wrap
new file mode 100755
index 00000000000..894b424de36
--- /dev/null
+++ b/Master/texmf-dist/doc/support/latexdiff/contrib/latexdiff-wrap
@@ -0,0 +1,192 @@
+#!/bin/bash
+#
+# latexdiff-wrap
+#
+# Wrapper for latexdiff, to
+#   * provide support for documents consiting of more than 1 latex file
+#   * provide my common arguments
+#
+# Copyright (C) by Volker Kuhlmann <VolkerKuhlmann@gmx.de>
+# Released under the terms of the GNU General Public License (GPL) Version 2.
+# See http://www.gnu.org/ for details.
+#
+# Volker Kuhlmann
+#   5, 6, 7, 12, 16, 17 Oct 2005
+#   31 Jan; 5, 7, 13, 15 Feb 2006
+#
+
+VERSION="0.6, 15 Feb 2006"
+AUTHOR="Volker Kuhlmann <VolkerKuhlmann@gmx.de>"
+COPYRIGHT="Copyright (C) 2005-2006"
+
+
+####
+#### Constants and initialised variables
+#
+diffcmd="latexdiff"
+diffrc="$HOME/texmf/latexdiff"
+#diffargs="-e latin1 --ignore-warnings -p latexdiff-preamble.sty"
+diffargs="-e latin1 --ignore-warnings"
+diffargs="$diffargs --append-safecmd $diffrc/safe-cmds"
+diffargs="$diffargs --append-textcmd $diffrc/text-cmds"
+# Note: Can't use multiple --append-safecmd
+# show current command lists:
+#diffcmd="$diffcmd --show-safecmd --show-textcmd --show-config"
+
+
+####
+#### Version, Usage, Help
+#
+show_version() {
+    echo "${0##*/} version $VERSION
+$COPYRIGHT by $AUTHOR"
+}
+
+show_usage() {
+    echo "
+Usage: ${0##*/} OLDDIR NEWDIR DIFFDIR [DIFFARGS --] FILE.tex [...]
+       ${0##*/} --show [DIFFARGS]
+Version $VERSION
+$COPYRIGHT by $AUTHOR
+"
+}
+
+show_help() {
+    show_usage
+    echo "\
+For each FILE.tex, build a new file DIFFDIR/FILE.tex with markup of the changes
+which were made from OLDDIR/FILE.tex to NEWDIR/FILE.tex.
+Any path given with FILE.tex is stripped off.
+Any DIFFARGS are added to the latexdiff call, if present (remember to follow
+them with a double-hyphen on its own before the FILE arguments).
+
+With --show, shows the settings latexdiff would be running with, including the
+changes applied by the user.
+"
+}
+
+# For scripts not using function library only:
+Version() { show_version; exitwith ErrVersion; }
+Usage() { show_help; exitwith ErrUsage; }
+Help() { test "$1" && exitwith ErrHelp show_help; show_help; exitwith ErrOK; }
+
+
+####
+#### Error/Exit codes
+#
+exitwith() {
+    exec 1>&2  # write stdout on stderr instead
+  case "$1" in
+    ErrOK)
+    	exit 0;;
+    ErrVersion|ErrUsage|ErrHelp)
+	# Output generated by function (program) $2, if given
+	test -n "$2" && "$2"
+	exit 1;;
+ # more codes in here
+ # more codes in here
+    ErrBadoption)
+    	echo "Bad option '$2'."
+	echo "Call with -h for help."
+	exit 9;;
+    ErrMissingParameter)
+	echo "A required parameter for option $2 is missing."
+	echo "Call with -h for help."
+	exit 9;;
+    *)
+	echo "Internal error: exitwith() called with illegal error code '$1'."
+	exit 19;;
+  esac
+}
+
+
+####
+#### Parse command line parameters
+#
+
+# If the next arg starts with a "-", collect additional argument for latexdiff
+# until "--".
+scanextraargs() {
+    addargs=()
+    case "$1" in -*)
+	while [ $# -gt 0 -a "$1" != "--" ]; do
+    	    addargs=( "${addargs[@]}" "$1" )
+	    shift
+	done
+	test "$1" == "--" && shift
+    ;; esac
+    fileargs=( "$@" )
+}
+
+case "$1" in
+    --version)	    	Version;;
+    --usage)	    	Usage;;
+    --help|-h|-help)	Help;;
+    --show)
+        shift
+	scanextraargs "$@"
+	(set -x
+	$diffcmd $diffargs "${addargs[@]}" \
+	    --show-safecmd --show-textcmd --show-config 
+	) | fmt
+    	exit $? ;;
+esac
+
+olddir="${1%/}"
+newdir="${2%/}"
+diffdir="${3%/}"
+
+if ! [ -d "$olddir" -a -d "$newdir" -a -d "$diffdir" ]; then
+    Help 1>&2 err
+fi
+
+shift 3
+
+scanextraargs "$@"
+set -- "${fileargs[@]}"
+
+
+
+####
+#### Functions
+#
+#set -x
+Log() { echo 1>&2 "+ $@"; "$@"; }
+
+
+####
+#### Main
+#
+
+# Create output directory, just in case.
+(set -x
+mkdir -p "$diffdir"
+)
+while [ $# -gt 0 ]; do
+    file="${1##*/}"
+    echo Examining: "$file"
+    # No point running latexdiff if both files are identical,
+    # but run latexdiff on top-level LaTeX file in any case.
+    if cmp --quiet "$olddir/$file" "$newdir/$file" \
+	&& ! grep -lq '\\begin.*{document}' "$newdir/$file"; then
+	(set -x
+	cp -p "$olddir/$file" "$diffdir"
+	)
+    else
+    	# Delete file, to make sure it's not clobbered by redirecting stdout
+	# in case it's a symlink to te original.
+	test -f "$diffdir/$file" && (set -x
+	rm "$diffdir/$file"
+	)
+	# Run latexdiff if both input files are present.
+	run=1
+	test -f "$olddir/$file" || { echo 1>&2 "No file: $olddir/$file"; run=; }
+	test -f "$newdir/$file" || { echo 1>&2 "No file: $newdir/$file"; run=; }
+	test -n "$run" && \
+	(set -x
+	$diffcmd $diffargs "${addargs[@]}" \
+	    "$olddir/$file" "$newdir/$file"  > "$diffdir/$file"
+	)
+    fi
+    shift
+done
diff --git a/Master/texmf-dist/doc/support/latexdiff/contrib/latexdiff.spec b/Master/texmf-dist/doc/support/latexdiff/contrib/latexdiff.spec
new file mode 100644
index 00000000000..9255a69fea9
--- /dev/null
+++ b/Master/texmf-dist/doc/support/latexdiff/contrib/latexdiff.spec
@@ -0,0 +1,58 @@
+Summary: Diff for LaTeX files
+Name: latexdiff
+Version: 0.5
+Release: 1
+License: GPL
+Group: Productivity/Publishing/TeX/Utilities
+URL: http://www.tug.org/tex-archive/help/Catalogue/entries/latexdiff.html
+Source0: %{name}.zip
+BuildArch: noarch
+BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root
+# only required for 'make install-ext'
+# Requires: perl-Algorithm-Diff
+
+
+%description
+latexdiff is a Perl script, which compares two latex files and marks
+up significant differences between them (i.e. a diff for latex files).
+  Various options are available for visual markup using standard latex
+packages such as "color.sty". Changes not directly affecting visible
+text, for example in formatting commands, are still marked in
+the latex source.
+
+(C) 2004 Frederik Tilmann <tilmann@esc.cam.ac.uk>
+
+
+%prep
+%setup -n %{name}
+
+
+%build
+# quick had to adapt the Makefile
+%{__mv} Makefile Makefile.old
+%{__sed} \
+  -e "s;INSTALLPATH = /usr/local;INSTALLPATH = \${DESTDIR}%{_prefix};" \
+  -e "s;INSTALLMANPATH = \$(INSTALLPATH)/man;INSTALLMANPATH = \${DESTDIR}%{_mandir};" \
+  Makefile.old > Makefile
+
+
+%install
+%{__mkdir_p} $RPM_BUILD_ROOT%{_bindir}
+%{__mkdir_p} $RPM_BUILD_ROOT%{_mandir}/man1
+
+%makeinstall
+
+
+%clean
+[ "${RPM_BUILD_ROOT}" != "/" ] && [ -d "${RPM_BUILD_ROOT}" ] && %{__rm} -rf "${RPM_BUILD_ROOT}"
+
+
+%files
+%defattr(-,root,root)
+%doc example CHANGES LICENSE README
+%{_bindir}/*
+%{_mandir}/man*/*
+
+%changelog
+* Thu Jan  4 2007 Till Dörges <till@doerges.net> - 0.5-1
+- Initial build.
diff --git a/Master/texmf-dist/doc/support/latexdiff/doc/example-diff.tex b/Master/texmf-dist/doc/support/latexdiff/doc/example-diff.tex
index a4764813b58..7166571f398 100644
--- a/Master/texmf-dist/doc/support/latexdiff/doc/example-diff.tex
+++ b/Master/texmf-dist/doc/support/latexdiff/doc/example-diff.tex
@@ -1,7 +1,7 @@
 \documentclass[12pt,a4paper]{article}
 %DIF LATEXDIFF DIFFERENCE FILE
-%DIF DEL example-draft.tex   Sun Jan 27 23:50:07 2013
-%DIF ADD example-rev.tex     Sun Jan 27 23:50:07 2013
+%DIF DEL example-draft.tex   Thu Jun 12 00:01:26 2014
+%DIF ADD example-rev.tex     Thu Jun 12 00:01:26 2014
 
 \setlength{\topmargin}{-0.2in}
 \setlength{\textheight}{9.5in}
diff --git a/Master/texmf-dist/doc/support/latexdiff/doc/latexdiff-man.pdf b/Master/texmf-dist/doc/support/latexdiff/doc/latexdiff-man.pdf
index 30242d8b36a..a3d640adfe2 100644
--- a/Master/texmf-dist/doc/support/latexdiff/doc/latexdiff-man.pdf
+++ b/Master/texmf-dist/doc/support/latexdiff/doc/latexdiff-man.pdf
diff --git a/Master/texmf-dist/doc/support/latexdiff/latexdiff b/Master/texmf-dist/doc/support/latexdiff/latexdiff
index febae2d5be1..717a0933a2f 100755
--- a/Master/texmf-dist/doc/support/latexdiff/latexdiff
+++ b/Master/texmf-dist/doc/support/latexdiff/latexdiff
@@ -3,9 +3,9 @@
 # latexdiff - differences two latex files on the word level
 #             and produces a latex file with the differences marked up.
 #
-#   Copyright (C) 2004-12  F J Tilmann (tilmann@gfz-potsdam.de, ftilmann@users.berlios.de)
+#   Copyright (C) 2004-12  F J Tilmann (tilmann@gfz-potsdam.de)
 #
-# Project webpages:   http://latexdiff.berlios.de/
+# Repository/issue tracker:   https://github.com/ftilmann/latexdiff
 # CTAN page:          http://www.ctan.org/tex-archive/support/latexdiff
 #
 #    This program is free software: you can redistribute it and/or modify
@@ -22,14 +22,34 @@
 #
 # Detailed usage information at the end of the file
 #
+# ToDo:
+#
+# Version 1.0.4
+#    - introduce list UNSAFEMATHCMD, which holds list of commands which cannot be marked up with \DIFadd or \DIFdel commands  (only relevant for WHOLE and COARSE math markup modes)
+#    - new subtype LABEL which gives each change a label. This can later be used to only display pages where changes
+#      have been made (instructions for that are put as comments into the diff'ed file) inspired by answer on http://tex.stackexchange.com/questions/166049/invisible-markers-in-pdfs-using-pdflatex
+#    - Configuration variables take into accout some commands from additional packages: 
+#      tikzpicture environment now treated as PICTUREENV, and \smallmatrix in ARRENV (amsmath)
+#    - --flatten: support for \subfile command (subfiles package)  (in response to http://tex.stackexchange.com/questions/167620/latexdiff-with-subfiles )
+#    - --flatten: \bibliography commands expand if corresponding bbl file present
+#    - angled bracket optional commands now parsed correctly (patch #3570) submitted by Dave Kleinschmidt (thanks)
+#    - \RequirePackage now treated as synonym of \usepackage with respect to setting packages
+#    - special rules for apacite package (redefine citation commands)
+#    - recognise /dev/null as 'file-like' arguments for --preamble and --config options
+#    - fix units package incompatibility with ulem for text maths statements $ ..$ (thanks to Stuart Prescott for reporting this)
+#    - amsmath environment cases treated correctly (Bug fix #19029) (thanks to Jalar)
+#    - {,} in comments no longer confuse latexdiff (Bug fix #19146)
+#    - \% in one-letter sub/Superscripts was not converted correctly
+#
 # Version 1.0.3
 #    - fix bug in add_safe_commands that made latexdiff hang on DeclareMathOperator 
 #      command in preamble
-#    - \(..\) inline math expressions were not parsed correctly, if the contained a linebreak
+#    - \(..\) inline math expressions were not parsed correctly, if they contained a linebreak
 #    - applied patch contributed by tomflannaghan via Berlios: [ Patch #3431 ] Adds correct handling of \left< and \right>
 #    - \$ is treated correctly as a literal dollar sign (thanks to Reed Cartwright and Joshua Miller for reporting this bug 
-#       and sketching out the solution)
-#    - \^ and \_ are correctly interpreted as accent and underlined space, respectively, not as superscript of subscript (thanks to Wail Yahyaoui for pointing out this bug)
+#      and sketching out the solution)
+#    - \^ and \_ are correctly interpreted as accent and underlined space, respectively, not as superscript of subscript
+#      (thanks to Wail Yahyaoui for pointing out this bug)
 #
 # Version 1.0.1 - treat \big,\bigg etc. equivalently to \left and
 #              \right - include starred version in MATHENV - apply
@@ -92,28 +112,30 @@ my ($algodiffversion)=split(/ /,$Algorithm::Diff::VERSION);
 
 
 my ($versionstring)=<<EOF ;
-This is LATEXDIFF 1.0.3  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
-  (c) 2004-2013 F J Tilmann
+This is LATEXDIFF 1.0.4  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
+  (c) 2004-2014 F J Tilmann
 EOF
 
 # Configuration variables: these have to be visible from the subroutines
 my $MINWORDSBLOCK=3; # minimum number of tokens to form an independent block
                      # shorter identical blocks will be merged to the previous word
 my $FLOATENV='(?:figure|table|plate)[\w\d*@]*' ;   # Environments in which FL variants of defined commands are used
-my $PICTUREENV='(?:picture|DIFnomarkup)[\w\d*@]*' ;   # Environments in which all change markup is removed
+my $PICTUREENV='(?:picture|tikzpicture|DIFnomarkup)[\w\d*@]*' ;   # Environments in which all change markup is removed
 my $MATHENV='(?:equation[*]?|displaymath|DOLLARDOLLAR)[*]?' ;           # Environments turning on display math mode (code also knows about \[ and \])
 my $MATHREPL='displaymath';  # Environment introducing deleted maths blocks
 my $MATHARRENV='(?:eqnarray|align|alignat|gather|multline|flalign)[*]?' ;           # Environments turning on eqnarray math mode
 my $MATHARRREPL='eqnarray*';  # Environment introducing deleted maths blocks
-my $ARRENV='(?:array|[pbvBV]matrix)'; # Environments making arrays in math mode.  The underlining style does not cope well with those - as a result in-text math environments are surrounded by \mbox{ } if any of these commands is used in an inline math block
+my $ARRENV='(?:array|[pbvBV]?matrix|smallmatrix|cases|split)'; # Environments making arrays in math mode.  The underlining style does not cope well with those - as a result in-text math environments are surrounded by \mbox{ } if any of these commands is used in an inline math block
 my $COUNTERCMD='(?:footnote|part|chapter|section|subsection|subsubsection|paragraph|subparagraph)';  # textcmds which are associated with a counter
                                         # If any of these commands occur in a deleted block
                                         # they will be succeeded by an \addtocounter{...}{-1}
                                         # for the associated counter such that the overall numbers
                                         # should be the same as in the new file
+my @UNSAFEMATHCMD=('qedhere');           # Commands which are definitely unsafe for marking up (amsmath qedhere only tested to not work with UNDERLINE markup)
 my $CITECMD=0 ;  # \cite-type commands which need to be protected within an mbox in UNDERLINE and other modes using ulem; pattern simply designed to never match; will be overwritten later for selected styles
 my $CITE2CMD=0;  # \cite-type commands which should be reinstated in deleted blocks
-
+my $MBOXINLINEMATH=0; # if set to 1 then surround marked-up inline maths expression with \mbox ( to get around compatibility
+                      # problems between some maths packages and ulem package
 
 
 # Markup strings
@@ -176,7 +198,7 @@ my ($type,$subtype,$floattype,$config,$preamblefile,$encoding,$nolabel,$visiblel
     $replacecontext1,$appendcontext1,
     $replacecontext2,$appendcontext2,
     $help,$verbose,$driver,$version,$ignorewarnings,
-    $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug);  ###$disablemathmark,
+    $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug,$earlylatexdiffpreamble);  ###$disablemathmark,
 # MNEMNONICS for mathmarkup
 my $mathmarkup;
 use constant {
@@ -205,6 +227,11 @@ $mathmarkup=COARSE;
 $verbose=0;
 # output debug and intermediate files, set to 0 in final distribution
 $debug=0; 
+# insert preamble directly after documentclass - experimental feature, set to 0 in final distribution
+# Note that this failed with mini example (or other files, where packages used in latexdiff preamble
+# are called again with incompatible options in preamble of resulting file)
+$earlylatexdiffpreamble=0;
+
 # define character properties
 sub IsNonAsciiPunct { return <<'END'    # Unicode punctuation but excluding ASCII punctuation
 +utf8::IsPunct
@@ -312,29 +339,6 @@ foreach $excludesafe ( @excludesafelist ) {
   init_regex_arr_ext(\@SAFECMDEXCL, $excludesafe);
 }
 
-# Special: treat all cite commands as safe except in UNDERLINE and FONTSTRIKE mode
-# (there is a conflict between citation and ulem package, see
-# package documentation)
-# Use post-processing
-
-if ( uc($type) ne "UNDERLINE" && uc($type) ne "FONTSTRIKE" && uc($type) ne "CULINECHBAR" ) {
-  push (@SAFECMDLIST, qr/^cite.*$/);
-} else {
-  ### Experimental: disable text and emph commands
-  push (@SAFECMDLIST, qr/^cite.*$/) unless $disablecitmark;
-  push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
-  # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
-  if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
-    # remove \cite command again from list of safe commands
-    pop @SAFECMDLIST;
-    # deleted cite commands
-    $CITE2CMD='(?:cite\w*|nocite)' unless $disablecitmark ; # \cite-type commands which should be reinstated in deleted blocks
-  } else {
-    $CITECMD='(?:cite\w*|nocite)' unless $disablecitmark ; # \cite commands which need to be protected within an mbox in UNDERLINE and other modes using ulem
-  }
-}
-$CITECMD='(?:cite\w*|nocite)' if $enablecitmark ; # as above for explicit selection
-
 # setting up @TEXTCMDLIST and @TEXTCMDEXCL
 if (defined($replacetext)) {
   init_regex_arr_ext(\@TEXTCMDLIST,$replacetext);
@@ -373,7 +377,7 @@ foreach $appendcontext2 ( @appendcontext2list ) {
 # setting configuration variables
 @config=();
 foreach $config ( @configlist ) {
-  if (-f $config ) {
+  if (-f $config || lc $config eq '/dev/null' ) {
     open(FILE,$config) or die ("Couldn't open configuration file $config: $!");
     while (<FILE>) {
       chomp;
@@ -484,6 +488,7 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $pat5 = '(?:[^{}]|\{'.$pat4.'\})*';
   my $pat6 = '(?:[^{}]|\{'.$pat5.'\})*';
   my $brat0 = '(?:[^\[\]]|\\\[|\\\])*'; 
+  my $abrat0 = '(?:[^<>])*';
 
   my $quotemarks = '(?:\'\')|(?:\`\`)';
   my $punct='[0.,\/\'\`:;\"\?\(\)\[\]!~\p{IsNonAsciiPunct}\p{IsNonAsciiS}]';
@@ -495,7 +500,7 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $word='(?:[-\w\d*]|\\\\[\"\'\`~^][A-Za-z\*])+';
   my $cmdleftright='\\\\(?:left|right|[Bb]igg?[lrm]?|middle)\s*(?:[<>()\[\]|]|\\\\(?:[|{}]|\w+))';
 
-  my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
+  my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:<'.$abrat0.'>|\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
   my $backslashnl='\\\\\n';
   my $oneletcmd='\\\\.\*?(?:\['.$brat0.'\]|\{'. $pat6 . '\})*';
   my $math='\$(?:[^$]|\\\$)*?\$|\\\\[(](?:.|\n)*?\\\\[)]';
@@ -504,8 +509,6 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $comment='%.*?\n';
   my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
 
-
-
 # now we are done setting up and can start working   
 my ($oldfile, $newfile) = @ARGV;
 # check for existence of input files
@@ -559,6 +562,9 @@ if ($flatten) {
   $newbody=flatten($newbody,$newpreamble,$newfile,$encoding);
 }
 
+
+
+
 my @auxlines;
 if ( length $oldpreamble && length $newpreamble ) {
   # pre-process preamble by looking for commands used in \maketitle (title, author, date etc commands) 
@@ -572,13 +578,25 @@ if ( length $oldpreamble && length $newpreamble ) {
   # Base this assessment on the new preamble
   add_safe_commands($newpreamble);
 
+  # get a list of packages from preamble if not predefine
   %packages=list_packages(@newpreamble) unless %packages;
+  ###  if ( %packages ) {print STDERR "DEBUG Packages: ",%packages,"\n" ;}
   if (defined $packages{"hyperref"} ) {
+    # deleted lines should not generate or appear in link names:
     print STDERR "hyperref package detected.\n" if $verbose ;
     $latexdiffpreamble =~ s/\{\\DIFadd\}/{\\DIFaddtex}/g;
     $latexdiffpreamble =~ s/\{\\DIFdel\}/{\\DIFdeltex}/g;
     $latexdiffpreamble .= join "\n",(extrapream("HYPERREF"),"");
   }
+
+  if (defined $packages{"units"}  && ( $latexdiffpreamble =~ /\\RequirePackage(?:\[$brat0\])?\{ulem\}/ ) ) {
+    # protect inlined maths environments by surrounding with an \mbox
+    # this is done to get around an incompatibility between the ulem and units package
+    # where spaces in the argument to underlined or crossed-out \unit commands cause an error message
+    print STDERR "units package detected at the same time as style using ulem.\n" if $verbose ;
+    $MBOXINLINEMATH=1;
+  }
+
   print STDERR "Differencing preamble.\n" if $verbose;
 
   # insert dummy first line such that line count begins with line 1 (rather than perl's line 0) - just so that line numbers inserted by linediff are correct
@@ -596,7 +614,14 @@ if ( length $oldpreamble && length $newpreamble ) {
     push @diffpreamble,"%DIF DELETED TITLE COMMANDS FOR MARKUP";
     push @diffpreamble,join("\n",@auxlines);
   }
-  push @diffpreamble,$latexdiffpreamble;
+  if ( $earlylatexdiffpreamble) {
+    # insert latexdiff command directly after documentclass at beginning of preamble
+    # note that grep is only run for its side effect
+    ( grep { s/^([^%]*\\documentclass.*)$/$1$latexdiffpreamble/ } @diffpreamble )==1 or die "Could not find documentclass statement in preamble";
+  } else {
+    # insert latexdiff commands at the end of preamble (default behaviour)
+    push @diffpreamble,$latexdiffpreamble;
+  }
   push @diffpreamble,'\begin{document}';
 }
 elsif ( !length $oldpreamble && !length $newpreamble ) {
@@ -606,6 +631,43 @@ elsif ( !length $oldpreamble && !length $newpreamble ) {
   exit(2);
 }
 
+# Special: treat all cite commands as safe except in UNDERLINE and FONTSTRIKE mode
+# (there is a conflict between citation and ulem package, see
+# package documentation)
+# Use post-processing
+# and $packages{"apacite"}!~/natbibpapa/
+my ($citpat,$citpatsafe);
+
+if ( defined $packages{"apacite"}  ) {
+  print STDERR "DEBUG apacite citation commands\n"  if $debug;
+  $citpatsafe=qr/^(?:mask)?(?:full|short)?cite(?:A|author|year)?(?:NP)?$/;
+  $citpat='(?:mask)?(?:full|short|no)?cite(?:A|author|year|meta)?(?:NP)?';
+} else {
+  # citation command pattern for all other citation schemes
+  $citpatsafe=qr/^cite.*$/;
+  $citpat='(?:cite\w*|nocite)';
+};
+
+if ( uc($type) ne "UNDERLINE" && uc($type) ne "FONTSTRIKE" && uc($type) ne "CULINECHBAR" ) {
+  push (@SAFECMDLIST, $citpatsafe);
+} else {
+  ### Experimental: disable text and emph commands
+  push (@SAFECMDLIST, $citpatsafe) unless $disablecitmark;
+  push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
+  # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
+  if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
+    # remove \cite command again from list of safe commands
+    pop @SAFECMDLIST;
+    # deleted cite commands
+    $CITE2CMD=$citpat unless $disablecitmark ; # \cite-type commands which should be reinstated in deleted blocks
+  } else {
+    $CITECMD=$citpat unless $disablecitmark ; # \cite commands which need to be protected within an mbox in UNDERLINE and other modes using ulem
+  }
+}
+$CITECMD=$citpat if $enablecitmark ; # as above for explicit selection
+
+print STDERR "CITECMD:|$CITECMD|\n" if $debug;
+
 if (defined $packages{"amsmath"}  or defined $packages{"amsart"} or defined $packages{"amsbook"} ) {
   print STDERR "amsmath package detected.\n" if $verbose ;
   $MATHARRREPL='align*';
@@ -697,7 +759,7 @@ sub read_file_with_encoding {
 }
 
 # %packages=list_packages(@preamble)
-# scans the arguments for \documentclass and \usepackage statements and constructs a hash
+# scans the arguments for \documentclass,\RequirePackage and \usepackage statements and constructs a hash
 # whose keys are the included packages, and whose values are the associated optional arguments
 sub list_packages {
   my (@preamble)=@_;
@@ -705,7 +767,7 @@ sub list_packages {
   foreach $line ( @preamble ) {
     # get rid of comments
     $line=~s/(?<!\\)%.*$// ;
-    if ( $line =~ m/\\(?:documentclass|usepackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
+    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
 #      print STDERR "Found something: |$line|\n";
       if (defined($1)) {
 	$packages{$2}=$1;
@@ -742,7 +804,7 @@ sub add_safe_commands {
       }
     }
 
-    while ( $preamble =~ m/\\(?:|re|provide)newcommand\s*{\\(\w*)\}(?:|\[\d*\])\s*\{(${pat6})\}/osg ) {
+    while ( $preamble =~ m/\\(?:new|renew|provide)command\s*{\\(\w*)\}(?:|\[\d*\])\s*\{(${pat6})\}/osg ) {
       my $maybe_to_test  = $1;
       my $should_be_safe = $2;
       my $success = 0;
@@ -772,14 +834,20 @@ sub add_safe_commands {
 
 # flatten($text,$preamble,$filename,$encoding)
 # expands \input and \include commands within text
+# expands \bibliography command with corresponding bbl file if available
+# expands \subfile command (from subfiles package - not part of standard text distribution)
 # preamble is scanned for includeonly commands
 # encoding is the encoding
 sub flatten {
   my ($text,$preamble,$filename,$encoding)=@_;
-  my ($includeonly,$dirname,$fname,$newpage,$replacement,$begline);
+  my ($includeonly,$dirname,$fname,$newpage,$replacement,$begline,$bblfile,$subfile);
+  my ($subpreamble,$subbody,$subpost);
   require File::Basename ; 
   require File::Spec ; 
   $dirname = File::Basename::dirname($filename);
+  $bblfile = $filename;
+  $bblfile=~s/\.tex$//;
+  $bblfile.=".bbl";
 
   if ( ($includeonly) = ($preamble =~ m/\\includeonly{(.*?)}/ ) ) {
     $includeonly =~ s/,/|/g;
@@ -789,9 +857,10 @@ sub flatten {
 
   print STDERR "DEBUG: includeonly $includeonly\n" if $debug;
 
+  # recursively replace \\input and \\include files
   $text=~s/(^(?:[^%\n]|\\%)*)\\input{(.*?)}|\\include{(${includeonly}(?:\.tex)?)}/{ 
 	    $fname = $2 if defined($2) ;
-	    $fname = $3 if defined($3) ;       
+	    $fname = $3 if defined($3) ;
             #      # add tex extension unless there is a three letter extension already 
             $fname .= ".tex" unless $fname =~ m|\.\w{3}|;
             print STDERR "DEBUG Beg of line match |$1|\n" if defined($1) && $debug ;
@@ -805,6 +874,34 @@ sub flatten {
 	    $newpage=(defined($3)? " \\newpage " : "") ;
 	    "$begline$newpage$replacement$newpage";
           }/exgm;
+  # replace bibliography with bbl file if it exists
+  $text=~s/(^(?:[^%\n]|\\%)*)\\bibliography{(.*?)}/{ 
+           if ( -f $bblfile ){
+	     $replacement=read_file_with_encoding(File::Spec->catfile($bblfile), $encoding);
+	   } else {
+	     warn "Bibliography file $bblfile cannot be found. No flattening of \\bibliography done. Run bibtex on old and new files first";
+	     $replacement="\\bibliography{$2}";
+	   }
+	   $begline=(defined($1)? $1 : "") ;
+	   "$begline$replacement";
+  }/exgm;
+  # replace subfile with contents (subfile package)
+  $text=~s/(^(?:[^%\n]|\\%)*)\\subfile{(.*?)}/{ 
+	   $fname = $2; 
+           #      # add tex extension unless there is a three letter extension already 
+           $fname .= ".tex" unless $fname =~ m|\.\w{3}|;
+           print STDERR "DEBUG Beg of line match |$1|\n" if defined($1) && $debug ;
+           print STDERR "Include file as subfile $fname\n" if $verbose;
+           print STDERR "DEBUG looking for file ",File::Spec->catfile($dirname,$fname), "\n" if $debug;
+           # content of file becomes replacement value (use recursion)
+           # now strip away everything outside and including \begin{document} and \end{document} pair#
+	   #             # note: no checking for comments is made
+           $subfile=read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
+           ($subpreamble,$subbody,$subpost)=splitdoc($subfile,'\\\\begin\{document\}','\\\\end\{document\}');
+	   $replacement=flatten($subbody, $preamble,$filename,$encoding);
+           $begline=(defined($1)? $1 : "") ;
+	   "$begline$replacement";
+  }/exgm;
 
   return($text);
 }
@@ -830,7 +927,7 @@ sub extrapream {
   while (@_) {
     $copy=0;
     $type=shift ;
-    if ( -f $type ) {
+    if ( -f $type || lc $type eq '/dev/null' ) {
       open (FILE,$type) or die "Cannot open preamble file $type: $!";
       print STDERR "Reading preamble file $type\n" if $verbose ;
       while (<FILE>) {
@@ -1398,7 +1495,7 @@ sub marktags {
 	  # Keep these commands even in deleted blocks, hence set $opencmd and $closecmd (5th and 6th argument of marktags) to 
 	  # ""
 	  local @SAFECMDLIST=(".*"); 
-	  local @SAFECMDEXCL=('\\','\\\\');
+	  local @SAFECMDEXCL=('\\','\\\\',@UNSAFEMATHCMD);
 	  push(@$retval,$command,marktags("","",$open,$close,"","",$comment,\@argtext)#@argtext
                        ,$closingbracket);
         } else {
@@ -1433,9 +1530,8 @@ sub marktags {
 # preprocess($string, ..)
 # carry out the following pre-processing steps for all arguments:
 # 1. Remove leading white-space
-#    Change \{ to \LEFTBRACE and \} to \RIGHTBRACE
-# #. change begin and end commands  within comments to BEGINDIF, ENDDIF
-#    so they don't disturb the pattern matching (if there are several \begin or \end in one line
+#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
+# #.   Change {,} in comments to \CLEFTBRACE, \CRIGHTBRACE
 # 2. mark all first empty line (in block of several) with \PAR tokens
 # 3. Convert all '\%' into '\PERCENTAGE ' and all '\$' into \DOLLAR to make parsing regular expressions easier
 # 4. Convert all \verb|some verbatim text| commands (where | can be an arbitrary character)
@@ -1462,11 +1558,9 @@ sub preprocess {
     #    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
     s/(?<!\\)\\{/\\QLEFTBRACE /sg;
     s/(?<!\\)\\}/\\QRIGHTBRACE /sg;
-    # change begin and end commands  within comments such that they
-    # don't disturb the pattern matching (if there are several \begin or \end in one line
-    # this substitution is insufficient but that appears unlikely)
-    s/(%.*)\\begin\{(.*)$/$1\\BEGINDIF\{$2/mg ;
-    s/(%.*)\\end\{(.*)$/$1\\ENDDIF\{$2/mg ;
+# replace {,} in comments with \\CLEFTBRACE,\\CRIGHTBRACE
+    1 while s/((?<!\\)%.*)\{(.*)$/$1\\CLEFTBRACE $2/mg ;
+    1 while s/((?<!\\)%.*)\}(.*)$/$1\\CRIGHTBRACE $2/mg ;
 
     s/\n(\s*?)\n((?:\s*\n)*)/\n$1\\PAR\n$2/g ;
     s/(?<!\\)\\%/\\PERCENTAGE /g ;  # (?<! is negative lookbehind assertion to prevent \\% from being converted
@@ -1579,7 +1673,7 @@ sub fromhash {
 # 9.. remove all \PAR tokens
 # 10.  package specific processing:  endfloat: make sure \begin{figure} and \end{figure} are always
 #      on a line by themselves, similarly for table environment
-#  4, undo renaming of the \begin and \end in comments
+#  4, undo renaming of the \begin, \end,{,}  in comments
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
 #
 # Note have to manually synchronize substitution commands below and 
@@ -1705,8 +1799,14 @@ sub postprocess {
       }
       # or protect \cite commands with \mbox
       if ($CITECMD) {
-	$delblock=~s/(\\($CITECMD)${extraspace}(?:\[$brat0\]${extraspace}){0,2}\{$pat6\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	$delblock=~s/(\\($CITECMD)${extraspace}(?:<$abrat0>${extraspace})?(?:\[$brat0\]${extraspace}){0,2}\{$pat6\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
       } 
+      # if MBOXINLINEMATH is set, protect inlined math environments with an extra mbox
+      if ( $MBOXINLINEMATH ) {
+	# note additional \newline after command is omitted from output if right at the end of deleted block (otherwise a spurious empty line is generated)
+	$delblock=~s/($math)(?:[\s\n]*)?/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
+      }
+
 #     splice in modified delblock
       substr($_,$begin,$len)=$delblock;
       pos = $begin + length($delblock);
@@ -1728,7 +1828,16 @@ sub postprocess {
       }
       if ($CITECMD) {
 	my $addblockbefore=$addblock;
-	$addblock=~ s/(\\($CITECMD)${extraspace}(?:\[$brat0\]${extraspace}){0,2}\{$pat2\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	#(?:mask)?(?:full|short|no)?cite(?:A|author|year|meta)(?:NP)?$/
+	###my $CITECMD; $CITECMD="cite(?:A)$";
+	$addblock=~ s/(\\($CITECMD)${extraspace}(?:<$abrat0>${extraspace})?(?:\[$brat0\]${extraspace}){0,2}\{$pat2\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	print STDERR "DEBUG: CITECMD $CITECMD\nDEBUG: addblock before:|$addblockbefore|\n" if $debug;
+	print STDERR "DEBUG: addblock after: |$addblock|\n" if $debug;
+      }
+      # if MBOXINLINEMATH is set, protect inlined math environments with an extra mbox
+      if ( $MBOXINLINEMATH ) {
+	##$addblock=~s/($math)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
+	$addblock=~s/($math)(?:[\s\n]*)?/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
       }
 #     splice in modified addblock
       substr($_,$begin,$len)=$addblock;
@@ -1736,13 +1845,6 @@ sub postprocess {
     }
 
 
-    ### old place for BEGINDIF, ENDDIF replacement
-    # change begin and end commands  within comments such that they
-    # don't disturb the pattern matching (if there are several \begin or \end in one line
-    # this substitution is insufficient but that appears unlikely)
-    # This needs to be repeated here to also get rid of DIFdelcmd-protected environments
-    s/(%.*)\\begin\{(.*)$/$1\\BEGINDIF\{$2/mg ;
-    s/(%.*)\\end\{(.*)$/$1\\ENDDIF\{$2/mg ;
 
     # Replace MATHMODE environments from step 1a above by the correct Math environment
 
@@ -1809,8 +1911,8 @@ sub postprocess {
     s/(\\verb\*?)\{([-\d]*?)\}/"${1}". fromhash(\%verbhash,$2)/esg;
     s/${DELCMDOPEN}\\(verbatim\*?)\{([-\d]*?)\}/"${DELCMDOPEN}\\begin{${1}}".fromhash(\%verbhash,$2,$DELCMDOPEN)."${DELCMDOPEN}\\end{${1}}"/esg;
     s/\\(verbatim\*?)\{([-\d]*?)\}/"\\begin{${1}}".fromhash(\%verbhash,$2)."\\end{${1}}"/esg;
-    # Convert '\PERCENTAGE ' back into '\%'			       
-    s/\\PERCENTAGE /\\%/g;
+    # Convert '\PERCENTAGE ' back into '\%' (the final question mark catches a special situation where due to a latter pre-processing step the ' ' becomes separated	       
+    s/\\PERCENTAGE ?/\\%/g;
     # Convert '\DOLLAR ' back into '\$'			       
     s/\\DOLLAR /\\\$/g;
     # remove all \PAR tokens (taking care to properly keep commented out PAR's
@@ -1833,9 +1935,7 @@ sub postprocess {
       # split lines with remaining characters after float enviroment conmmand
       s/(\\(?:begin|end)\{(?:figure|table)\})(.+)$/$1\n$2/mg;
     }
-    # undo renaming of the \begin and \end  and dollars in comments 
-    s/(%.*)\\BEGINDIF\{(.*)$/$1\\begin\{$2/mg ;
-    s/(%.*)\\ENDDIF\{(.*)$/$1\\end\{$2/mg ;
+    # undo renaming of the \begin and \end,{,}  and dollars in comments 
     1 while s/(%.*)DOLLARDIF/$1\$/mg ;
     # undo renaming of the \cite.. commands in comments 
     if ( $CITECMD ) {
@@ -1847,11 +1947,15 @@ sub postprocess {
 # 4. Convert \begin{DOLLARDOLLAR} \end{DOLLARDOLLAR} into $$ $$
     s/\\begin\{DOLLARDOLLAR\}(.*?)\\end\{DOLLARDOLLAR\}/\$\$$1\$\$/sg;
 # 5. Convert  \SUPERSCRIPTNB{n} into ^n  and  \SUPERSCRIPT{nn} into ^{nnn}
-    1 while s/\\SUPERSCRIPTNB{($pat0)}/^$1/g ;
     1 while s/\\SUPERSCRIPT{($pat6)}/^{$1}/g ;
+    1 while s/\\SUPERSCRIPTNB{($pat0)}/^$1/g ;
     # Convert  \SUBSCRIPNB{n} into _n  and  \SUBCRIPT{nn} into _{nnn}
-    1 while s/\\SUBSCRIPTNB{($pat0)}/_$1/g ;
     1 while s/\\SUBSCRIPT{($pat6)}/_{$1}/g ;
+    1 while s/\\SUBSCRIPTNB{($pat0)}/_$1/g ;
+    1 while s/(%.*)\\CRIGHTBRACE (.*)$/$1\}$2/mg ;
+    1 while s/(%.*)\\CLEFTBRACE (.*)$/$1\{$2/mg ;
+
+
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
     s/\\QLEFTBRACE /\\{/sg;
     s/\\QRIGHTBRACE /\\}/sg;
@@ -2114,7 +2218,7 @@ format as new.tex but has all changes relative to old.tex marked up or commented
 --subtype=markstyle
 -s markstyle           Add code to preamble for selected style for bracketing
                        commands (e.g. to mark changes in  margin)
-                       Available styles: SAFE MARGINAL DVIPSCOL COLOR
+                       Available styles: SAFE MARGINAL DVIPSCOL COLOR LABEL
                        [ Default: SAFE ]
 
 --floattype=markstyle
@@ -2213,7 +2317,7 @@ format as new.tex but has all changes relative to old.tex marked up or commented
                        Use of the --packages option disables automatic scanning, so if for any
                        reason package specific parsing needs to be switched off, use --packages=none.
                        The following packages trigger special behaviour:
-                       endfloat hyperref amsmath
+                       endfloat hyperref amsmath apacite
                        [ Default: scan the preamble for \\usepackage commands to determine
                          loaded packages.]
 
@@ -2269,7 +2373,7 @@ Miscelleneous options
 
 --no-label             Suppress inclusion of old and new file names as comment in output file
 
---visble-label         Include old and new filenames (or labels set with --label option) as 
+--visible-label         Include old and new filenames (or labels set with --label option) as 
                        visible output
 
 --flatten              Replace \\input and \\include commands within body by the content
@@ -2294,7 +2398,6 @@ Miscelleneous options
 
 --version              Show version number.
 
-For further information, consult   http://latexdiff.berlios.de
 EOF
 }
 
@@ -2457,7 +2560,7 @@ B<-s markstyle>
 Add code to preamble for selected style for bracketing
 commands (e.g. to mark changes in  margin). This option defines
 C<\DIFaddbegin>, C<\DIFaddend>, C<\DIFdelbegin> and C<\DIFdelend> commands.
-Available styles: C<SAFE MARGINAL COLOR DVIPSCOL>
+Available styles: C<SAFE MARGINAL COLOR DVIPSCOL LABEL>
 
 [ Default: C<SAFE> ]
 
@@ -2526,6 +2629,10 @@ define new C<\DIFadd> and C<\DIFdel> commands, which provide a wrapper for these
 using them for the text but not for the link defining command (where any markup would cause
 errors).
 
+=item C<apacite>
+
+Redefine the commands recognised as citation commands.
+
 =back
 
 [ Default: scan the preamble for C<\\usepackage> commands to determine
@@ -2698,6 +2805,7 @@ Protect citation commands in changed sections with \\mbox command [i.e. use defa
 =head2 Miscellaneous
 
 =over 4
+
 =item B<--verbose> or B<-V>
 
 Output various status information to stderr during processing.
@@ -2962,9 +3070,7 @@ Option allow-spaces not implemented entirely consistently. It breaks
 the rules that number and type of white space does not matter, as
 different numbers of inter-argument spaces are treated as significant.
 
-Please submit bug reports on the latexdiff project page I<http://latexdiff.berlios.de>, 
-send them to user discussion list C<latexdiff-users@lists.berlios,de> (prior subscription 
-to list required, also on project webpage)
+Please submit bug reports using the issue tracker of the github repository page I<https://github.com/ftilmann/latexdiff.git>, 
 or send them to I<tilmann@gfz-potsdam.de>.  Include the serial number of I<latexdiff>
 (from comments at the top of the source or use B<--version>).  If you come across latex
 files that are error-free and conform to the specifications set out
@@ -2992,7 +3098,7 @@ I<latexdiff-fast> requires the I<diff> command to be present.
 
 =head1 AUTHOR
 
-Version 1.0.2
+Version 1.0.4
 Copyright (C) 2004-2012 Frederik Tilmann
 
 This program is free software; you can redistribute it and/or modify
@@ -3000,7 +3106,7 @@ it under the terms of the GNU General Public License Version 3
 
 Contributors of fixes and additions: V. Kuhlmann, J. Paisley, N. Becker, T. Doerges, K. Huebner, 
 T. Connors, Sebastian Gouezel and many others.
-Thanks to the many people who send in bug reports, feature suggestions, and other feedback.
+Thanks to the many people who sent in bug reports, feature suggestions, and other feedback.
 
 =cut
 
@@ -3373,7 +3479,26 @@ institute
 \providecommand{\DIFdelend}{\protect\color{black}}
 %DIF END COLOR PREAMBLE
 
-
+%DIF LABEL PREAMBLE
+% To show only pages with changes (pdf) (external program pdftk needs to be installed)
+% (only works for simple documents with non-repeated page numbers)
+% pdflatex diff.tex
+% pdflatex diff.tex
+% pdftk diff.pdf cat `perl -lne 'if (m/\\newlabel{DIFchg[be]\d*}{{.*}{(.*)}}/) { print $1 }' diff.aux | uniq | tr -s \\n ' '` output diff-changedpages.pdf
+% To show only pages with changes (dvips/dvipdf)
+% latex diff.tex
+% latex diff.tex
+% dvips -pp `perl -lne 'if (m/\\newlabel{DIFchg[be]\d*}{{.*}{(.*)}}/) { print $1 }' diff.aux | uniq | tr -s \\n ','` diff.dvi 
+\typeout{Check comments in preamble of output for instructions how to show only pages where changes have been made}
+\newcount\DIFcounterb
+\global\DIFcounterb 0\relax
+\newcount\DIFcountere
+\global\DIFcountere 0\relax
+\providecommand{\DIFaddbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}} %DIF PREAMBLE
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}} %DIF PREAMBLE
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}} %DIF PREAMBLE
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}} %DIF PREAMBLE
+%DIF END LABEL PREAMBLE
 %% FLOAT TYPES 
 
 %DIF FLOATSAFE PREAMBLE
@@ -3403,7 +3528,7 @@ institute
 \providecommand{\DIFaddendFL}{}
 \providecommand{\DIFdelbeginFL}{}
 \providecommand{\DIFdelendFL}{}
-%DIF END FLOATSAFE PREAMBLE
+%DIF END TRADITIONALSAFE PREAMBLE
 
 %% SPECIAL PACKAGE PREAMBLE COMMANDS
 
diff --git a/Master/texmf-dist/doc/support/latexdiff/latexdiff-fast b/Master/texmf-dist/doc/support/latexdiff/latexdiff-fast
index e53afc12fe6..22f2f8f0344 100755
--- a/Master/texmf-dist/doc/support/latexdiff/latexdiff-fast
+++ b/Master/texmf-dist/doc/support/latexdiff/latexdiff-fast
@@ -3,9 +3,9 @@
 # latexdiff - differences two latex files on the word level
 #             and produces a latex file with the differences marked up.
 #
-#   Copyright (C) 2004-12  F J Tilmann (tilmann@gfz-potsdam.de, ftilmann@users.berlios.de)
+#   Copyright (C) 2004-12  F J Tilmann (tilmann@gfz-potsdam.de)
 #
-# Project webpages:   http://latexdiff.berlios.de/
+# Repository/issue tracker:   https://github.com/ftilmann/latexdiff
 # CTAN page:          http://www.ctan.org/tex-archive/support/latexdiff
 #
 #    This program is free software: you can redistribute it and/or modify
@@ -22,14 +22,34 @@
 #
 # Detailed usage information at the end of the file
 #
+# ToDo:
+#
+# Version 1.0.4
+#    - introduce list UNSAFEMATHCMD, which holds list of commands which cannot be marked up with \DIFadd or \DIFdel commands  (only relevant for WHOLE and COARSE math markup modes)
+#    - new subtype LABEL which gives each change a label. This can later be used to only display pages where changes
+#      have been made (instructions for that are put as comments into the diff'ed file) inspired by answer on http://tex.stackexchange.com/questions/166049/invisible-markers-in-pdfs-using-pdflatex
+#    - Configuration variables take into accout some commands from additional packages: 
+#      tikzpicture environment now treated as PICTUREENV, and \smallmatrix in ARRENV (amsmath)
+#    - --flatten: support for \subfile command (subfiles package)  (in response to http://tex.stackexchange.com/questions/167620/latexdiff-with-subfiles )
+#    - --flatten: \bibliography commands expand if corresponding bbl file present
+#    - angled bracket optional commands now parsed correctly (patch #3570) submitted by Dave Kleinschmidt (thanks)
+#    - \RequirePackage now treated as synonym of \usepackage with respect to setting packages
+#    - special rules for apacite package (redefine citation commands)
+#    - recognise /dev/null as 'file-like' arguments for --preamble and --config options
+#    - fix units package incompatibility with ulem for text maths statements $ ..$ (thanks to Stuart Prescott for reporting this)
+#    - amsmath environment cases treated correctly (Bug fix #19029) (thanks to Jalar)
+#    - {,} in comments no longer confuse latexdiff (Bug fix #19146)
+#    - \% in one-letter sub/Superscripts was not converted correctly
+#
 # Version 1.0.3
 #    - fix bug in add_safe_commands that made latexdiff hang on DeclareMathOperator 
 #      command in preamble
-#    - \(..\) inline math expressions were not parsed correctly, if the contained a linebreak
+#    - \(..\) inline math expressions were not parsed correctly, if they contained a linebreak
 #    - applied patch contributed by tomflannaghan via Berlios: [ Patch #3431 ] Adds correct handling of \left< and \right>
 #    - \$ is treated correctly as a literal dollar sign (thanks to Reed Cartwright and Joshua Miller for reporting this bug 
-#       and sketching out the solution)
-#    - \^ and \_ are correctly interpreted as accent and underlined space, respectively, not as superscript of subscript (thanks to Wail Yahyaoui for pointing out this bug)
+#      and sketching out the solution)
+#    - \^ and \_ are correctly interpreted as accent and underlined space, respectively, not as superscript of subscript
+#      (thanks to Wail Yahyaoui for pointing out this bug)
 #
 # Version 1.0.1 - treat \big,\bigg etc. equivalently to \left and
 #              \right - include starred version in MATHENV - apply
@@ -653,28 +673,30 @@ my ($algodiffversion)=split(/ /,$Algorithm::Diff::VERSION);
 
 
 my ($versionstring)=<<EOF ;
-This is LATEXDIFF 1.0.3  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
-  (c) 2004-2013 F J Tilmann
+This is LATEXDIFF 1.0.4  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
+  (c) 2004-2014 F J Tilmann
 EOF
 
 # Configuration variables: these have to be visible from the subroutines
 my $MINWORDSBLOCK=3; # minimum number of tokens to form an independent block
                      # shorter identical blocks will be merged to the previous word
 my $FLOATENV='(?:figure|table|plate)[\w\d*@]*' ;   # Environments in which FL variants of defined commands are used
-my $PICTUREENV='(?:picture|DIFnomarkup)[\w\d*@]*' ;   # Environments in which all change markup is removed
+my $PICTUREENV='(?:picture|tikzpicture|DIFnomarkup)[\w\d*@]*' ;   # Environments in which all change markup is removed
 my $MATHENV='(?:equation[*]?|displaymath|DOLLARDOLLAR)[*]?' ;           # Environments turning on display math mode (code also knows about \[ and \])
 my $MATHREPL='displaymath';  # Environment introducing deleted maths blocks
 my $MATHARRENV='(?:eqnarray|align|alignat|gather|multline|flalign)[*]?' ;           # Environments turning on eqnarray math mode
 my $MATHARRREPL='eqnarray*';  # Environment introducing deleted maths blocks
-my $ARRENV='(?:array|[pbvBV]matrix)'; # Environments making arrays in math mode.  The underlining style does not cope well with those - as a result in-text math environments are surrounded by \mbox{ } if any of these commands is used in an inline math block
+my $ARRENV='(?:array|[pbvBV]?matrix|smallmatrix|cases|split)'; # Environments making arrays in math mode.  The underlining style does not cope well with those - as a result in-text math environments are surrounded by \mbox{ } if any of these commands is used in an inline math block
 my $COUNTERCMD='(?:footnote|part|chapter|section|subsection|subsubsection|paragraph|subparagraph)';  # textcmds which are associated with a counter
                                         # If any of these commands occur in a deleted block
                                         # they will be succeeded by an \addtocounter{...}{-1}
                                         # for the associated counter such that the overall numbers
                                         # should be the same as in the new file
+my @UNSAFEMATHCMD=('qedhere');           # Commands which are definitely unsafe for marking up (amsmath qedhere only tested to not work with UNDERLINE markup)
 my $CITECMD=0 ;  # \cite-type commands which need to be protected within an mbox in UNDERLINE and other modes using ulem; pattern simply designed to never match; will be overwritten later for selected styles
 my $CITE2CMD=0;  # \cite-type commands which should be reinstated in deleted blocks
-
+my $MBOXINLINEMATH=0; # if set to 1 then surround marked-up inline maths expression with \mbox ( to get around compatibility
+                      # problems between some maths packages and ulem package
 
 
 # Markup strings
@@ -737,7 +759,7 @@ my ($type,$subtype,$floattype,$config,$preamblefile,$encoding,$nolabel,$visiblel
     $replacecontext1,$appendcontext1,
     $replacecontext2,$appendcontext2,
     $help,$verbose,$driver,$version,$ignorewarnings,
-    $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug);  ###$disablemathmark,
+    $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug,$earlylatexdiffpreamble);  ###$disablemathmark,
 # MNEMNONICS for mathmarkup
 my $mathmarkup;
 use constant {
@@ -766,6 +788,11 @@ $mathmarkup=COARSE;
 $verbose=0;
 # output debug and intermediate files, set to 0 in final distribution
 $debug=0; 
+# insert preamble directly after documentclass - experimental feature, set to 0 in final distribution
+# Note that this failed with mini example (or other files, where packages used in latexdiff preamble
+# are called again with incompatible options in preamble of resulting file)
+$earlylatexdiffpreamble=0;
+
 # define character properties
 sub IsNonAsciiPunct { return <<'END'    # Unicode punctuation but excluding ASCII punctuation
 +utf8::IsPunct
@@ -873,29 +900,6 @@ foreach $excludesafe ( @excludesafelist ) {
   init_regex_arr_ext(\@SAFECMDEXCL, $excludesafe);
 }
 
-# Special: treat all cite commands as safe except in UNDERLINE and FONTSTRIKE mode
-# (there is a conflict between citation and ulem package, see
-# package documentation)
-# Use post-processing
-
-if ( uc($type) ne "UNDERLINE" && uc($type) ne "FONTSTRIKE" && uc($type) ne "CULINECHBAR" ) {
-  push (@SAFECMDLIST, qr/^cite.*$/);
-} else {
-  ### Experimental: disable text and emph commands
-  push (@SAFECMDLIST, qr/^cite.*$/) unless $disablecitmark;
-  push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
-  # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
-  if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
-    # remove \cite command again from list of safe commands
-    pop @SAFECMDLIST;
-    # deleted cite commands
-    $CITE2CMD='(?:cite\w*|nocite)' unless $disablecitmark ; # \cite-type commands which should be reinstated in deleted blocks
-  } else {
-    $CITECMD='(?:cite\w*|nocite)' unless $disablecitmark ; # \cite commands which need to be protected within an mbox in UNDERLINE and other modes using ulem
-  }
-}
-$CITECMD='(?:cite\w*|nocite)' if $enablecitmark ; # as above for explicit selection
-
 # setting up @TEXTCMDLIST and @TEXTCMDEXCL
 if (defined($replacetext)) {
   init_regex_arr_ext(\@TEXTCMDLIST,$replacetext);
@@ -934,7 +938,7 @@ foreach $appendcontext2 ( @appendcontext2list ) {
 # setting configuration variables
 @config=();
 foreach $config ( @configlist ) {
-  if (-f $config ) {
+  if (-f $config || lc $config eq '/dev/null' ) {
     open(FILE,$config) or die ("Couldn't open configuration file $config: $!");
     while (<FILE>) {
       chomp;
@@ -1045,6 +1049,7 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $pat5 = '(?:[^{}]|\{'.$pat4.'\})*';
   my $pat6 = '(?:[^{}]|\{'.$pat5.'\})*';
   my $brat0 = '(?:[^\[\]]|\\\[|\\\])*'; 
+  my $abrat0 = '(?:[^<>])*';
 
   my $quotemarks = '(?:\'\')|(?:\`\`)';
   my $punct='[0.,\/\'\`:;\"\?\(\)\[\]!~\p{IsNonAsciiPunct}\p{IsNonAsciiS}]';
@@ -1056,7 +1061,7 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $word='(?:[-\w\d*]|\\\\[\"\'\`~^][A-Za-z\*])+';
   my $cmdleftright='\\\\(?:left|right|[Bb]igg?[lrm]?|middle)\s*(?:[<>()\[\]|]|\\\\(?:[|{}]|\w+))';
 
-  my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
+  my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:<'.$abrat0.'>|\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
   my $backslashnl='\\\\\n';
   my $oneletcmd='\\\\.\*?(?:\['.$brat0.'\]|\{'. $pat6 . '\})*';
   my $math='\$(?:[^$]|\\\$)*?\$|\\\\[(](?:.|\n)*?\\\\[)]';
@@ -1065,8 +1070,6 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $comment='%.*?\n';
   my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
 
-
-
 # now we are done setting up and can start working   
 my ($oldfile, $newfile) = @ARGV;
 # check for existence of input files
@@ -1120,6 +1123,9 @@ if ($flatten) {
   $newbody=flatten($newbody,$newpreamble,$newfile,$encoding);
 }
 
+
+
+
 my @auxlines;
 if ( length $oldpreamble && length $newpreamble ) {
   # pre-process preamble by looking for commands used in \maketitle (title, author, date etc commands) 
@@ -1133,13 +1139,25 @@ if ( length $oldpreamble && length $newpreamble ) {
   # Base this assessment on the new preamble
   add_safe_commands($newpreamble);
 
+  # get a list of packages from preamble if not predefine
   %packages=list_packages(@newpreamble) unless %packages;
+  ###  if ( %packages ) {print STDERR "DEBUG Packages: ",%packages,"\n" ;}
   if (defined $packages{"hyperref"} ) {
+    # deleted lines should not generate or appear in link names:
     print STDERR "hyperref package detected.\n" if $verbose ;
     $latexdiffpreamble =~ s/\{\\DIFadd\}/{\\DIFaddtex}/g;
     $latexdiffpreamble =~ s/\{\\DIFdel\}/{\\DIFdeltex}/g;
     $latexdiffpreamble .= join "\n",(extrapream("HYPERREF"),"");
   }
+
+  if (defined $packages{"units"}  && ( $latexdiffpreamble =~ /\\RequirePackage(?:\[$brat0\])?\{ulem\}/ ) ) {
+    # protect inlined maths environments by surrounding with an \mbox
+    # this is done to get around an incompatibility between the ulem and units package
+    # where spaces in the argument to underlined or crossed-out \unit commands cause an error message
+    print STDERR "units package detected at the same time as style using ulem.\n" if $verbose ;
+    $MBOXINLINEMATH=1;
+  }
+
   print STDERR "Differencing preamble.\n" if $verbose;
 
   # insert dummy first line such that line count begins with line 1 (rather than perl's line 0) - just so that line numbers inserted by linediff are correct
@@ -1157,7 +1175,14 @@ if ( length $oldpreamble && length $newpreamble ) {
     push @diffpreamble,"%DIF DELETED TITLE COMMANDS FOR MARKUP";
     push @diffpreamble,join("\n",@auxlines);
   }
-  push @diffpreamble,$latexdiffpreamble;
+  if ( $earlylatexdiffpreamble) {
+    # insert latexdiff command directly after documentclass at beginning of preamble
+    # note that grep is only run for its side effect
+    ( grep { s/^([^%]*\\documentclass.*)$/$1$latexdiffpreamble/ } @diffpreamble )==1 or die "Could not find documentclass statement in preamble";
+  } else {
+    # insert latexdiff commands at the end of preamble (default behaviour)
+    push @diffpreamble,$latexdiffpreamble;
+  }
   push @diffpreamble,'\begin{document}';
 }
 elsif ( !length $oldpreamble && !length $newpreamble ) {
@@ -1167,6 +1192,43 @@ elsif ( !length $oldpreamble && !length $newpreamble ) {
   exit(2);
 }
 
+# Special: treat all cite commands as safe except in UNDERLINE and FONTSTRIKE mode
+# (there is a conflict between citation and ulem package, see
+# package documentation)
+# Use post-processing
+# and $packages{"apacite"}!~/natbibpapa/
+my ($citpat,$citpatsafe);
+
+if ( defined $packages{"apacite"}  ) {
+  print STDERR "DEBUG apacite citation commands\n"  if $debug;
+  $citpatsafe=qr/^(?:mask)?(?:full|short)?cite(?:A|author|year)?(?:NP)?$/;
+  $citpat='(?:mask)?(?:full|short|no)?cite(?:A|author|year|meta)?(?:NP)?';
+} else {
+  # citation command pattern for all other citation schemes
+  $citpatsafe=qr/^cite.*$/;
+  $citpat='(?:cite\w*|nocite)';
+};
+
+if ( uc($type) ne "UNDERLINE" && uc($type) ne "FONTSTRIKE" && uc($type) ne "CULINECHBAR" ) {
+  push (@SAFECMDLIST, $citpatsafe);
+} else {
+  ### Experimental: disable text and emph commands
+  push (@SAFECMDLIST, $citpatsafe) unless $disablecitmark;
+  push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
+  # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
+  if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
+    # remove \cite command again from list of safe commands
+    pop @SAFECMDLIST;
+    # deleted cite commands
+    $CITE2CMD=$citpat unless $disablecitmark ; # \cite-type commands which should be reinstated in deleted blocks
+  } else {
+    $CITECMD=$citpat unless $disablecitmark ; # \cite commands which need to be protected within an mbox in UNDERLINE and other modes using ulem
+  }
+}
+$CITECMD=$citpat if $enablecitmark ; # as above for explicit selection
+
+print STDERR "CITECMD:|$CITECMD|\n" if $debug;
+
 if (defined $packages{"amsmath"}  or defined $packages{"amsart"} or defined $packages{"amsbook"} ) {
   print STDERR "amsmath package detected.\n" if $verbose ;
   $MATHARRREPL='align*';
@@ -1258,7 +1320,7 @@ sub read_file_with_encoding {
 }
 
 # %packages=list_packages(@preamble)
-# scans the arguments for \documentclass and \usepackage statements and constructs a hash
+# scans the arguments for \documentclass,\RequirePackage and \usepackage statements and constructs a hash
 # whose keys are the included packages, and whose values are the associated optional arguments
 sub list_packages {
   my (@preamble)=@_;
@@ -1266,7 +1328,7 @@ sub list_packages {
   foreach $line ( @preamble ) {
     # get rid of comments
     $line=~s/(?<!\\)%.*$// ;
-    if ( $line =~ m/\\(?:documentclass|usepackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
+    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
 #      print STDERR "Found something: |$line|\n";
       if (defined($1)) {
 	$packages{$2}=$1;
@@ -1303,7 +1365,7 @@ sub add_safe_commands {
       }
     }
 
-    while ( $preamble =~ m/\\(?:|re|provide)newcommand\s*{\\(\w*)\}(?:|\[\d*\])\s*\{(${pat6})\}/osg ) {
+    while ( $preamble =~ m/\\(?:new|renew|provide)command\s*{\\(\w*)\}(?:|\[\d*\])\s*\{(${pat6})\}/osg ) {
       my $maybe_to_test  = $1;
       my $should_be_safe = $2;
       my $success = 0;
@@ -1333,14 +1395,20 @@ sub add_safe_commands {
 
 # flatten($text,$preamble,$filename,$encoding)
 # expands \input and \include commands within text
+# expands \bibliography command with corresponding bbl file if available
+# expands \subfile command (from subfiles package - not part of standard text distribution)
 # preamble is scanned for includeonly commands
 # encoding is the encoding
 sub flatten {
   my ($text,$preamble,$filename,$encoding)=@_;
-  my ($includeonly,$dirname,$fname,$newpage,$replacement,$begline);
+  my ($includeonly,$dirname,$fname,$newpage,$replacement,$begline,$bblfile,$subfile);
+  my ($subpreamble,$subbody,$subpost);
   require File::Basename ; 
   require File::Spec ; 
   $dirname = File::Basename::dirname($filename);
+  $bblfile = $filename;
+  $bblfile=~s/\.tex$//;
+  $bblfile.=".bbl";
 
   if ( ($includeonly) = ($preamble =~ m/\\includeonly{(.*?)}/ ) ) {
     $includeonly =~ s/,/|/g;
@@ -1350,9 +1418,10 @@ sub flatten {
 
   print STDERR "DEBUG: includeonly $includeonly\n" if $debug;
 
+  # recursively replace \\input and \\include files
   $text=~s/(^(?:[^%\n]|\\%)*)\\input{(.*?)}|\\include{(${includeonly}(?:\.tex)?)}/{ 
 	    $fname = $2 if defined($2) ;
-	    $fname = $3 if defined($3) ;       
+	    $fname = $3 if defined($3) ;
             #      # add tex extension unless there is a three letter extension already 
             $fname .= ".tex" unless $fname =~ m|\.\w{3}|;
             print STDERR "DEBUG Beg of line match |$1|\n" if defined($1) && $debug ;
@@ -1366,6 +1435,34 @@ sub flatten {
 	    $newpage=(defined($3)? " \\newpage " : "") ;
 	    "$begline$newpage$replacement$newpage";
           }/exgm;
+  # replace bibliography with bbl file if it exists
+  $text=~s/(^(?:[^%\n]|\\%)*)\\bibliography{(.*?)}/{ 
+           if ( -f $bblfile ){
+	     $replacement=read_file_with_encoding(File::Spec->catfile($bblfile), $encoding);
+	   } else {
+	     warn "Bibliography file $bblfile cannot be found. No flattening of \\bibliography done. Run bibtex on old and new files first";
+	     $replacement="\\bibliography{$2}";
+	   }
+	   $begline=(defined($1)? $1 : "") ;
+	   "$begline$replacement";
+  }/exgm;
+  # replace subfile with contents (subfile package)
+  $text=~s/(^(?:[^%\n]|\\%)*)\\subfile{(.*?)}/{ 
+	   $fname = $2; 
+           #      # add tex extension unless there is a three letter extension already 
+           $fname .= ".tex" unless $fname =~ m|\.\w{3}|;
+           print STDERR "DEBUG Beg of line match |$1|\n" if defined($1) && $debug ;
+           print STDERR "Include file as subfile $fname\n" if $verbose;
+           print STDERR "DEBUG looking for file ",File::Spec->catfile($dirname,$fname), "\n" if $debug;
+           # content of file becomes replacement value (use recursion)
+           # now strip away everything outside and including \begin{document} and \end{document} pair#
+	   #             # note: no checking for comments is made
+           $subfile=read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
+           ($subpreamble,$subbody,$subpost)=splitdoc($subfile,'\\\\begin\{document\}','\\\\end\{document\}');
+	   $replacement=flatten($subbody, $preamble,$filename,$encoding);
+           $begline=(defined($1)? $1 : "") ;
+	   "$begline$replacement";
+  }/exgm;
 
   return($text);
 }
@@ -1391,7 +1488,7 @@ sub extrapream {
   while (@_) {
     $copy=0;
     $type=shift ;
-    if ( -f $type ) {
+    if ( -f $type || lc $type eq '/dev/null' ) {
       open (FILE,$type) or die "Cannot open preamble file $type: $!";
       print STDERR "Reading preamble file $type\n" if $verbose ;
       while (<FILE>) {
@@ -1959,7 +2056,7 @@ sub marktags {
 	  # Keep these commands even in deleted blocks, hence set $opencmd and $closecmd (5th and 6th argument of marktags) to 
 	  # ""
 	  local @SAFECMDLIST=(".*"); 
-	  local @SAFECMDEXCL=('\\','\\\\');
+	  local @SAFECMDEXCL=('\\','\\\\',@UNSAFEMATHCMD);
 	  push(@$retval,$command,marktags("","",$open,$close,"","",$comment,\@argtext)#@argtext
                        ,$closingbracket);
         } else {
@@ -1994,9 +2091,8 @@ sub marktags {
 # preprocess($string, ..)
 # carry out the following pre-processing steps for all arguments:
 # 1. Remove leading white-space
-#    Change \{ to \LEFTBRACE and \} to \RIGHTBRACE
-# #. change begin and end commands  within comments to BEGINDIF, ENDDIF
-#    so they don't disturb the pattern matching (if there are several \begin or \end in one line
+#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
+# #.   Change {,} in comments to \CLEFTBRACE, \CRIGHTBRACE
 # 2. mark all first empty line (in block of several) with \PAR tokens
 # 3. Convert all '\%' into '\PERCENTAGE ' and all '\$' into \DOLLAR to make parsing regular expressions easier
 # 4. Convert all \verb|some verbatim text| commands (where | can be an arbitrary character)
@@ -2023,11 +2119,9 @@ sub preprocess {
     #    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
     s/(?<!\\)\\{/\\QLEFTBRACE /sg;
     s/(?<!\\)\\}/\\QRIGHTBRACE /sg;
-    # change begin and end commands  within comments such that they
-    # don't disturb the pattern matching (if there are several \begin or \end in one line
-    # this substitution is insufficient but that appears unlikely)
-    s/(%.*)\\begin\{(.*)$/$1\\BEGINDIF\{$2/mg ;
-    s/(%.*)\\end\{(.*)$/$1\\ENDDIF\{$2/mg ;
+# replace {,} in comments with \\CLEFTBRACE,\\CRIGHTBRACE
+    1 while s/((?<!\\)%.*)\{(.*)$/$1\\CLEFTBRACE $2/mg ;
+    1 while s/((?<!\\)%.*)\}(.*)$/$1\\CRIGHTBRACE $2/mg ;
 
     s/\n(\s*?)\n((?:\s*\n)*)/\n$1\\PAR\n$2/g ;
     s/(?<!\\)\\%/\\PERCENTAGE /g ;  # (?<! is negative lookbehind assertion to prevent \\% from being converted
@@ -2140,7 +2234,7 @@ sub fromhash {
 # 9.. remove all \PAR tokens
 # 10.  package specific processing:  endfloat: make sure \begin{figure} and \end{figure} are always
 #      on a line by themselves, similarly for table environment
-#  4, undo renaming of the \begin and \end in comments
+#  4, undo renaming of the \begin, \end,{,}  in comments
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
 #
 # Note have to manually synchronize substitution commands below and 
@@ -2266,8 +2360,14 @@ sub postprocess {
       }
       # or protect \cite commands with \mbox
       if ($CITECMD) {
-	$delblock=~s/(\\($CITECMD)${extraspace}(?:\[$brat0\]${extraspace}){0,2}\{$pat6\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	$delblock=~s/(\\($CITECMD)${extraspace}(?:<$abrat0>${extraspace})?(?:\[$brat0\]${extraspace}){0,2}\{$pat6\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
       } 
+      # if MBOXINLINEMATH is set, protect inlined math environments with an extra mbox
+      if ( $MBOXINLINEMATH ) {
+	# note additional \newline after command is omitted from output if right at the end of deleted block (otherwise a spurious empty line is generated)
+	$delblock=~s/($math)(?:[\s\n]*)?/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
+      }
+
 #     splice in modified delblock
       substr($_,$begin,$len)=$delblock;
       pos = $begin + length($delblock);
@@ -2289,7 +2389,16 @@ sub postprocess {
       }
       if ($CITECMD) {
 	my $addblockbefore=$addblock;
-	$addblock=~ s/(\\($CITECMD)${extraspace}(?:\[$brat0\]${extraspace}){0,2}\{$pat2\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	#(?:mask)?(?:full|short|no)?cite(?:A|author|year|meta)(?:NP)?$/
+	###my $CITECMD; $CITECMD="cite(?:A)$";
+	$addblock=~ s/(\\($CITECMD)${extraspace}(?:<$abrat0>${extraspace})?(?:\[$brat0\]${extraspace}){0,2}\{$pat2\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	print STDERR "DEBUG: CITECMD $CITECMD\nDEBUG: addblock before:|$addblockbefore|\n" if $debug;
+	print STDERR "DEBUG: addblock after: |$addblock|\n" if $debug;
+      }
+      # if MBOXINLINEMATH is set, protect inlined math environments with an extra mbox
+      if ( $MBOXINLINEMATH ) {
+	##$addblock=~s/($math)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
+	$addblock=~s/($math)(?:[\s\n]*)?/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
       }
 #     splice in modified addblock
       substr($_,$begin,$len)=$addblock;
@@ -2297,13 +2406,6 @@ sub postprocess {
     }
 
 
-    ### old place for BEGINDIF, ENDDIF replacement
-    # change begin and end commands  within comments such that they
-    # don't disturb the pattern matching (if there are several \begin or \end in one line
-    # this substitution is insufficient but that appears unlikely)
-    # This needs to be repeated here to also get rid of DIFdelcmd-protected environments
-    s/(%.*)\\begin\{(.*)$/$1\\BEGINDIF\{$2/mg ;
-    s/(%.*)\\end\{(.*)$/$1\\ENDDIF\{$2/mg ;
 
     # Replace MATHMODE environments from step 1a above by the correct Math environment
 
@@ -2370,8 +2472,8 @@ sub postprocess {
     s/(\\verb\*?)\{([-\d]*?)\}/"${1}". fromhash(\%verbhash,$2)/esg;
     s/${DELCMDOPEN}\\(verbatim\*?)\{([-\d]*?)\}/"${DELCMDOPEN}\\begin{${1}}".fromhash(\%verbhash,$2,$DELCMDOPEN)."${DELCMDOPEN}\\end{${1}}"/esg;
     s/\\(verbatim\*?)\{([-\d]*?)\}/"\\begin{${1}}".fromhash(\%verbhash,$2)."\\end{${1}}"/esg;
-    # Convert '\PERCENTAGE ' back into '\%'			       
-    s/\\PERCENTAGE /\\%/g;
+    # Convert '\PERCENTAGE ' back into '\%' (the final question mark catches a special situation where due to a latter pre-processing step the ' ' becomes separated	       
+    s/\\PERCENTAGE ?/\\%/g;
     # Convert '\DOLLAR ' back into '\$'			       
     s/\\DOLLAR /\\\$/g;
     # remove all \PAR tokens (taking care to properly keep commented out PAR's
@@ -2394,9 +2496,7 @@ sub postprocess {
       # split lines with remaining characters after float enviroment conmmand
       s/(\\(?:begin|end)\{(?:figure|table)\})(.+)$/$1\n$2/mg;
     }
-    # undo renaming of the \begin and \end  and dollars in comments 
-    s/(%.*)\\BEGINDIF\{(.*)$/$1\\begin\{$2/mg ;
-    s/(%.*)\\ENDDIF\{(.*)$/$1\\end\{$2/mg ;
+    # undo renaming of the \begin and \end,{,}  and dollars in comments 
     1 while s/(%.*)DOLLARDIF/$1\$/mg ;
     # undo renaming of the \cite.. commands in comments 
     if ( $CITECMD ) {
@@ -2408,11 +2508,15 @@ sub postprocess {
 # 4. Convert \begin{DOLLARDOLLAR} \end{DOLLARDOLLAR} into $$ $$
     s/\\begin\{DOLLARDOLLAR\}(.*?)\\end\{DOLLARDOLLAR\}/\$\$$1\$\$/sg;
 # 5. Convert  \SUPERSCRIPTNB{n} into ^n  and  \SUPERSCRIPT{nn} into ^{nnn}
-    1 while s/\\SUPERSCRIPTNB{($pat0)}/^$1/g ;
     1 while s/\\SUPERSCRIPT{($pat6)}/^{$1}/g ;
+    1 while s/\\SUPERSCRIPTNB{($pat0)}/^$1/g ;
     # Convert  \SUBSCRIPNB{n} into _n  and  \SUBCRIPT{nn} into _{nnn}
-    1 while s/\\SUBSCRIPTNB{($pat0)}/_$1/g ;
     1 while s/\\SUBSCRIPT{($pat6)}/_{$1}/g ;
+    1 while s/\\SUBSCRIPTNB{($pat0)}/_$1/g ;
+    1 while s/(%.*)\\CRIGHTBRACE (.*)$/$1\}$2/mg ;
+    1 while s/(%.*)\\CLEFTBRACE (.*)$/$1\{$2/mg ;
+
+
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
     s/\\QLEFTBRACE /\\{/sg;
     s/\\QRIGHTBRACE /\\}/sg;
@@ -2675,7 +2779,7 @@ format as new.tex but has all changes relative to old.tex marked up or commented
 --subtype=markstyle
 -s markstyle           Add code to preamble for selected style for bracketing
                        commands (e.g. to mark changes in  margin)
-                       Available styles: SAFE MARGINAL DVIPSCOL COLOR
+                       Available styles: SAFE MARGINAL DVIPSCOL COLOR LABEL
                        [ Default: SAFE ]
 
 --floattype=markstyle
@@ -2774,7 +2878,7 @@ format as new.tex but has all changes relative to old.tex marked up or commented
                        Use of the --packages option disables automatic scanning, so if for any
                        reason package specific parsing needs to be switched off, use --packages=none.
                        The following packages trigger special behaviour:
-                       endfloat hyperref amsmath
+                       endfloat hyperref amsmath apacite
                        [ Default: scan the preamble for \\usepackage commands to determine
                          loaded packages.]
 
@@ -2830,7 +2934,7 @@ Miscelleneous options
 
 --no-label             Suppress inclusion of old and new file names as comment in output file
 
---visble-label         Include old and new filenames (or labels set with --label option) as 
+--visible-label         Include old and new filenames (or labels set with --label option) as 
                        visible output
 
 --flatten              Replace \\input and \\include commands within body by the content
@@ -2855,7 +2959,6 @@ Miscelleneous options
 
 --version              Show version number.
 
-For further information, consult   http://latexdiff.berlios.de
 EOF
 }
 
@@ -3018,7 +3121,7 @@ B<-s markstyle>
 Add code to preamble for selected style for bracketing
 commands (e.g. to mark changes in  margin). This option defines
 C<\DIFaddbegin>, C<\DIFaddend>, C<\DIFdelbegin> and C<\DIFdelend> commands.
-Available styles: C<SAFE MARGINAL COLOR DVIPSCOL>
+Available styles: C<SAFE MARGINAL COLOR DVIPSCOL LABEL>
 
 [ Default: C<SAFE> ]
 
@@ -3087,6 +3190,10 @@ define new C<\DIFadd> and C<\DIFdel> commands, which provide a wrapper for these
 using them for the text but not for the link defining command (where any markup would cause
 errors).
 
+=item C<apacite>
+
+Redefine the commands recognised as citation commands.
+
 =back
 
 [ Default: scan the preamble for C<\\usepackage> commands to determine
@@ -3259,6 +3366,7 @@ Protect citation commands in changed sections with \\mbox command [i.e. use defa
 =head2 Miscellaneous
 
 =over 4
+
 =item B<--verbose> or B<-V>
 
 Output various status information to stderr during processing.
@@ -3523,9 +3631,7 @@ Option allow-spaces not implemented entirely consistently. It breaks
 the rules that number and type of white space does not matter, as
 different numbers of inter-argument spaces are treated as significant.
 
-Please submit bug reports on the latexdiff project page I<http://latexdiff.berlios.de>, 
-send them to user discussion list C<latexdiff-users@lists.berlios,de> (prior subscription 
-to list required, also on project webpage)
+Please submit bug reports using the issue tracker of the github repository page I<https://github.com/ftilmann/latexdiff.git>, 
 or send them to I<tilmann@gfz-potsdam.de>.  Include the serial number of I<latexdiff>
 (from comments at the top of the source or use B<--version>).  If you come across latex
 files that are error-free and conform to the specifications set out
@@ -3553,7 +3659,7 @@ I<latexdiff-fast> requires the I<diff> command to be present.
 
 =head1 AUTHOR
 
-Version 1.0.2
+Version 1.0.4
 Copyright (C) 2004-2012 Frederik Tilmann
 
 This program is free software; you can redistribute it and/or modify
@@ -3561,7 +3667,7 @@ it under the terms of the GNU General Public License Version 3
 
 Contributors of fixes and additions: V. Kuhlmann, J. Paisley, N. Becker, T. Doerges, K. Huebner, 
 T. Connors, Sebastian Gouezel and many others.
-Thanks to the many people who send in bug reports, feature suggestions, and other feedback.
+Thanks to the many people who sent in bug reports, feature suggestions, and other feedback.
 
 =cut
 
@@ -3934,7 +4040,26 @@ institute
 \providecommand{\DIFdelend}{\protect\color{black}}
 %DIF END COLOR PREAMBLE
 
-
+%DIF LABEL PREAMBLE
+% To show only pages with changes (pdf) (external program pdftk needs to be installed)
+% (only works for simple documents with non-repeated page numbers)
+% pdflatex diff.tex
+% pdflatex diff.tex
+% pdftk diff.pdf cat `perl -lne 'if (m/\\newlabel{DIFchg[be]\d*}{{.*}{(.*)}}/) { print $1 }' diff.aux | uniq | tr -s \\n ' '` output diff-changedpages.pdf
+% To show only pages with changes (dvips/dvipdf)
+% latex diff.tex
+% latex diff.tex
+% dvips -pp `perl -lne 'if (m/\\newlabel{DIFchg[be]\d*}{{.*}{(.*)}}/) { print $1 }' diff.aux | uniq | tr -s \\n ','` diff.dvi 
+\typeout{Check comments in preamble of output for instructions how to show only pages where changes have been made}
+\newcount\DIFcounterb
+\global\DIFcounterb 0\relax
+\newcount\DIFcountere
+\global\DIFcountere 0\relax
+\providecommand{\DIFaddbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}} %DIF PREAMBLE
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}} %DIF PREAMBLE
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}} %DIF PREAMBLE
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}} %DIF PREAMBLE
+%DIF END LABEL PREAMBLE
 %% FLOAT TYPES 
 
 %DIF FLOATSAFE PREAMBLE
@@ -3964,7 +4089,7 @@ institute
 \providecommand{\DIFaddendFL}{}
 \providecommand{\DIFdelbeginFL}{}
 \providecommand{\DIFdelendFL}{}
-%DIF END FLOATSAFE PREAMBLE
+%DIF END TRADITIONALSAFE PREAMBLE
 
 %% SPECIAL PACKAGE PREAMBLE COMMANDS