latexdiff

git-svn-id: svn://tug.org/texlive/trunk@36943 c570f23f-e606-0410-a88d-b1316a301751

9 files changed, 1463 insertions, 469 deletions

diff --git a/Master/texmf-dist/doc/support/latexdiff/Makefile b/Master/texmf-dist/doc/support/latexdiff/Makefile
index 45467307879..148ead25611 100644
--- a/Master/texmf-dist/doc/support/latexdiff/Makefile
+++ b/Master/texmf-dist/doc/support/latexdiff/Makefile
@@ -46,7 +46,7 @@ install-latexrevise:
 
 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-$$vcs ; done
+	cd $(INSTALLEXECPATH); for vcs in cvs rcs svn git hg ; do if [ -e latexdiff-$$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)"
diff --git a/Master/texmf-dist/doc/support/latexdiff/README b/Master/texmf-dist/doc/support/latexdiff/README
index e9e189350e0..911b585deec 100644
--- a/Master/texmf-dist/doc/support/latexdiff/README
+++ b/Master/texmf-dist/doc/support/latexdiff/README
@@ -12,10 +12,10 @@ latexrevise, which accepts or rejects all changes.  Manual
 editing of the difference file can be used to override this default
 behaviour and accept or reject selected changes only.  
 
-The author is F Tilmann (ftilmann@users.berlios.de). 
+The author is F Tilmann. 
 
-Project webpage:   http://latexdiff.berlios.de/
-CTAN page:          http://www.ctan.org/tex-archive/support/latexdiff
+Project webpage:   https://github.com/ftilmann/latexdiff/
+CTAN page:         http://www.ctan.org/pkg/latexdiff
 
 
 REQUIREMENTS
@@ -45,8 +45,8 @@ The basic installation procedure is almost trivial:
 
 2. Copy latexdiff.1 and latexrevise.1 into the correct man directory
 
-3. Optionally create soft links latexdiff-cvs latexdiff-rcs, and
-   latexdiff-svn for latexdiff-vc.
+3. Optionally create soft links latexdiff-cvs latexdiff-rcs, latexdiff-git
+   latexdiff-svn and latexdiff-hg for latexdiff-vc.
 
 The attached trivial Makefile contains example commands to carry out above 
 steps as root for a typical UNIX installation. Type 
@@ -91,7 +91,7 @@ latexdiff.spec (Author: T. Doerges) spec file for RPM generation
 latexchanges (Author: Jan-Ake Larsson) Wrapper script for applying latexdiff with numbered documen version 
 (see contrib/README.latexchanges for a more detailed description)
 
-Cntributions by the following authors were incorporated into the latexdiff code, or inspired me to 
+Contributions by the following authors were incorporated into the latexdiff code, or inspired me to 
 extend latexdiff in a similar way: J. Paisley, N. Becker, K. Huebner
 
 LICENSE (also see file COPYING)
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 a3d640adfe2..f30d1869c86 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/doc/latexdiff-man.tex b/Master/texmf-dist/doc/support/latexdiff/doc/latexdiff-man.tex
index b6bb37effe6..2adffccd99a 100644
--- a/Master/texmf-dist/doc/support/latexdiff/doc/latexdiff-man.tex
+++ b/Master/texmf-dist/doc/support/latexdiff/doc/latexdiff-man.tex
@@ -6,7 +6,7 @@
 %\setlength{\textwidth}{6.5in}
 %\setlength{\oddsidemargin}{0.0in}                                                                                  
 \title{Marking up differences between latex files with {\em latexdiff}}
-\author{F.J. Tilmann\thanks{tilmann@gfz-potsdam.de,ftilmann@users.berlios.de}}
+\author{F.J. Tilmann\thanks{tilmann@gfz-potsdam.de}}
 \date{\today}
 
 \begin{document}
diff --git a/Master/texmf-dist/doc/support/latexdiff/latexdiff b/Master/texmf-dist/doc/support/latexdiff/latexdiff
index 717a0933a2f..bb75ce4ac85 100755
--- a/Master/texmf-dist/doc/support/latexdiff/latexdiff
+++ b/Master/texmf-dist/doc/support/latexdiff/latexdiff
@@ -23,6 +23,19 @@
 # Detailed usage information at the end of the file
 #
 # ToDo:
+#      DONE
+#
+# Version 1.1.0
+#    - treat diacritics (\",\', etc) as safe commands
+#    - treat \_ and \& correctly as safe commands, even if used without spacing to the next word
+#    - Add a BOLD markup type that sets added text in bold face (Contribution by Victor Zabalza via pull request )
+#    - add append-mboxsafecmd list option to be able to specify special safe commands which need to be surrounded by mbox to avoid breaking (mostly this is needed with ulem package)
+#    - support for siunitx and cleveref packages: protect \SI command in siunitx package and \cref,\Cref{range}{*} in cleveref packages (thanks to Stefan Pinnow for testing)
+#    - experimental support for chemformula, mhchem packages: define \ch and \ce in packages as safe (but not \ch,\cee in equation array environments) - these unfortunately will not be marked up (thanks to Stefan Pinnow for testing)
+#    - bug fix: packages identified correctly even if \usepackage command options extend over several lines (previously \usepackage command needed to be fully contained in one line)
+#    - new subtype ONLYCHANGEDPAGE outputs only changed pages (might not work well for floating material)
+#    - new subtype ZLABEL operates similarly to LABEL but uses absolute page numbers (needs zref package)
+#    - undocumented option --debug/--nodebug to override default setting for debug mode (Default: 0 for release version, 1: for development version
 #
 # 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)
@@ -112,8 +125,8 @@ my ($algodiffversion)=split(/ /,$Algorithm::Diff::VERSION);
 
 
 my ($versionstring)=<<EOF ;
-This is LATEXDIFF 1.0.4  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
-  (c) 2004-2014 F J Tilmann
+This is LATEXDIFF 1.1.0  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
+  (c) 2004-2015 F J Tilmann
 EOF
 
 # Configuration variables: these have to be visible from the subroutines
@@ -132,8 +145,6 @@ my $COUNTERCMD='(?:footnote|part|chapter|section|subsection|subsubsection|paragr
                                         # 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
 
@@ -180,6 +191,9 @@ my @MATHTEXTCMDEXCL=();  #
 # Note I need to declare this with "our" instead of "my" because later in the code I have to "local"ise these  
 our @SAFECMDLIST=();  # array containing patterns of safe commands (which do not break when in the argument of DIFadd or DIFDEL)
 our @SAFECMDEXCL=();
+my @MBOXCMDLIST=();   # patterns for commands which are in principle safe but which need to be surrounded by an \mbox
+my @MBOXCMDEXCL=();           # all the patterns in MBOXCMDLIST will be appended to SAFECMDLIST
+
 
 my ($i,$j,$l);
 my ($old,$new);
@@ -199,6 +213,7 @@ my ($type,$subtype,$floattype,$config,$preamblefile,$encoding,$nolabel,$visiblel
     $replacecontext2,$appendcontext2,
     $help,$verbose,$driver,$version,$ignorewarnings,
     $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug,$earlylatexdiffpreamble);  ###$disablemathmark,
+my ($mboxsafe);
 # MNEMNONICS for mathmarkup
 my $mathmarkup;
 use constant {
@@ -208,9 +223,11 @@ use constant {
   FINE => 3
 };
 
+my ($mboxcmd);
 
 my (@configlist,@labels,
     @appendsafelist,@excludesafelist,
+    @appendmboxsafelist,@excludemboxsafelist,
     @appendtextlist,@excludetextlist,
     @appendcontext1list,@appendcontext2list,
     @packagelist);
@@ -219,9 +236,6 @@ my ($assign,@config);
 # the optional arguments to the package are the values of the hash elements
 my ($pkg,%packages);
 # Defaults
-$type='UNDERLINE';
-$subtype='SAFE';
-$floattype='FLOATSAFE';
 $mathmarkup=COARSE;
 
 $verbose=0;
@@ -267,6 +281,8 @@ GetOptions('type|t=s' => \$type,
 	   'append-context1cmd=s' => \@appendcontext1list,
 	   'replace-context2cmd=s' => \$replacecontext2,
 	   'append-context2cmd=s' => \@appendcontext2list,
+	   'exclude-mboxsafecmd=s' => \@excludemboxsafelist,
+	   'append-mboxsafecmd=s' => \@appendmboxsafelist,
 	   'show-preamble' => \$showpreamble,
 	   'show-safecmd' => \$showsafe,
 	   'show-textcmd' => \$showtext,
@@ -275,14 +291,15 @@ GetOptions('type|t=s' => \$type,
            'packages=s' => \@packagelist,
 	   'allow-spaces' => \$allowspaces,
            'math-markup=s' => \$mathmarkup,
-           'enable-citation-markup' => \$enablecitmark,
-           'disable-citation-markup' => \$disablecitmark,
+           'enable-citation-markup|enforce-auto-mbox' => \$enablecitmark,
+           'disable-citation-markup|disable-auto-mbox' => \$disablecitmark,
 	   'verbose|V' => \$verbose,
 	   'ignore-warnings' => \$ignorewarnings,
 	   'driver=s'=> \$driver,
 	   'flatten' => \$flatten,
 	   'version' => \$version,
-	   'help|h|H' => \$help);
+	   'help|h|H' => \$help,
+	   'debug!' => \$debug );
 
 if ( $help ) {
   usage() ;
@@ -298,6 +315,14 @@ print STDERR $versionstring if $verbose;
 if (defined($showall)){
   $showpreamble=$showsafe=$showtext=$showconfig=1;
 }
+# Default types
+$type='UNDERLINE' unless defined($type);
+$subtype='SAFE' unless defined($subtype);
+# set floattype to IDENTICAL for LABEL and ONLYCHANGEDPAGE subtype, unless it has been set explicitly on the command line
+$floattype=($subtype eq 'LABEL' || $subtype eq 'ONLYCHANGEDPAGE') ? 'IDENTICAL' : 'FLOATSAFE' unless defined($floattype);
+if ( $subtype eq 'LABEL' ) {
+  print STDERR "Note that LABEL subtype is deprecated. If possible, use ZLABEL instead (requires zref package)";
+}
 
 if (defined($mathmarkup)) {
   $mathmarkup=~tr/a-z/A-Z/;
@@ -338,6 +363,15 @@ foreach $appendsafe ( @appendsafelist ) {
 foreach $excludesafe ( @excludesafelist ) {
   init_regex_arr_ext(\@SAFECMDEXCL, $excludesafe);
 }
+# setting up @MBOXCMDLIST and @MBOXCMDEXCL
+foreach $mboxsafe ( @appendmboxsafelist ) {
+  init_regex_arr_ext(\@MBOXCMDLIST, $mboxsafe);
+}
+foreach $mboxsafe ( @excludemboxsafelist ) {
+  init_regex_arr_ext(\@MBOXCMDEXCL, $mboxsafe);
+}
+
+
 
 # setting up @TEXTCMDLIST and @TEXTCMDEXCL
 if (defined($replacetext)) {
@@ -496,18 +530,19 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $mathpunct='[+=<>\-\|]';
   my $and = '&';
   my $coords= '[\-.,\s\d]*';
+# quoted underscore - this needs special treatment as perl treats _ as a letter (\w) but latex does not
+# such that a\_b is interpreted as a{\_}b by latex but a{\_b} by perl
+  my $quotedunderscore='\\\\_';
 # word: sequence of letters or accents followed by letter
   my $word='(?:[-\w\d*]|\\\\[\"\'\`~^][A-Za-z\*])+';
   my $cmdleftright='\\\\(?:left|right|[Bb]igg?[lrm]?|middle)\s*(?:[<>()\[\]|]|\\\\(?:[|{}]|\w+))';
-
   my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:<'.$abrat0.'>|\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
   my $backslashnl='\\\\\n';
   my $oneletcmd='\\\\.\*?(?:\['.$brat0.'\]|\{'. $pat6 . '\})*';
   my $math='\$(?:[^$]|\\\$)*?\$|\\\\[(](?:.|\n)*?\\\\[)]';
 ## the current maths command cannot cope with newline within the math expression
-
   my $comment='%.*?\n';
-  my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
+  my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$quotedunderscore|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
 
 # now we are done setting up and can start working   
 my ($oldfile, $newfile) = @ARGV;
@@ -566,6 +601,10 @@ if ($flatten) {
 
 
 my @auxlines;
+
+# boolean variab
+my ($ulem)=0;
+
 if ( length $oldpreamble && length $newpreamble ) {
   # pre-process preamble by looking for commands used in \maketitle (title, author, date etc commands) 
   # and marking up content with latexdiff markup
@@ -579,22 +618,19 @@ if ( length $oldpreamble && length $newpreamble ) {
   add_safe_commands($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" ;}
+  %packages=list_packages($newpreamble) unless %packages;
+  if ( %packages && $debug ) { my $key ; foreach $key (keys %packages) { print STDERR "DEBUG \\usepackage[",$packages{$key},"]{",$key,"}\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;
+    ###    $latexdiffpreamble .= '%DIF PREAMBLE EXTENSION ADDED BY LATEXDIFF FOR HYPERREF PACKAGE' . "\n";
+    ###    $latexdiffpreamble .= '\providecommand{\DIFadd}[1]{\texorpdfstring{\DIFaddtex{#1}}{#1}}' . "\n";
+    ###    $latexdiffpreamble .= '\providecommand{\DIFdel}[1]{\texorpdfstring{\DIFdeltex{#1}}{}}' . "\n";
+    ###    $latexdiffpreamble .= '%DIF END PREAMBLE EXTENSION ADDED BY LATEXDIFF FOR HYPERREF PACKAGE' . "\n";
   }
 
   print STDERR "Differencing preamble.\n" if $verbose;
@@ -636,45 +672,116 @@ elsif ( !length $oldpreamble && !length $newpreamble ) {
 # package documentation)
 # Use post-processing
 # and $packages{"apacite"}!~/natbibpapa/
-my ($citpat,$citpatsafe);
+
+$ulem = ($latexdiffpreamble =~ /\\RequirePackage(?:\[$brat0\])?\{ulem\}/ || defined $packages{"ulem"});
+
+
+if (defined $packages{"units"}  && $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;
+}
+
+if (defined $packages{"siunitx"} ) {
+  # protect SI command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between the ulem and siunitx package
+  print STDERR "siunitx package detected.\n" if $verbose ;
+  my $mboxcmds='SI,ang,numlist,numrange,SIlist,SIrange';
+  init_regex_arr_ext(\@SAFECMDLIST,'num,si');
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"cleveref"} ) {
+  # protect selected command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between ulem and cleveref package
+  print STDERR "cleveref package detected.\n" if $verbose ;
+  my $mboxcmds='[Cc]ref(?:range)?\*?,labelcref,(?:lc)?name[cC]refs?' ;
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"glossaries"} ) {
+  # protect selected command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between ulem and glossaries package 
+  print STDERR "glossaries package detected.\n" if $verbose ;
+  my $mboxcmds='[gG][lL][sS](?:|pl|disp|link|first|firstplural|desc|user[iv][iv]?[iv]?),[aA][cC][rR](?:long|longpl|full|fullpl),[aA][cC][lfp]?[lfp]?';
+  init_regex_arr_ext(\@SAFECMDLIST,'[gG][lL][sS](?:(?:entry)?(?:text|plural|name|symbol)|displaynumberlist|entryfirst|entryfirstplural|entrydesc|entrydescplural|entrysymbolplural|entryuser[iv][iv]?[iv]?|entrynumberlist|entrydisplaynumberlist|entrylong|entrylongpl|entryshort|entryshortpl|entryfull|entryfullpl),[gG]lossentry(?:name|desc|symbol),[aA][cC][rR](?:short|shortpl),[aA]csp?');
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"chemformula"} ) {
+  print STDERR "chemformula package detected.\n" if $verbose ;
+  init_regex_arr_ext(\@SAFECMDLIST,'ch');
+  push(@UNSAFEMATHCMD,'ch');
+  # The next command would be needed to allow highlighting the interior of \ch commands in math environments
+  # but the redefinitions in chemformula are too deep to make this viable
+  # push(@MATHTEXTCMDLIST,'ch');
+}
+
+if (defined $packages{"mhchem"} ) {
+  print STDERR "mhchem package detected.\n" if $verbose ;
+  init_regex_arr_ext(\@SAFECMDLIST,'ce');
+  push(@UNSAFEMATHCMD,'cee');
+  # The next command would be needed to allow highlighting the interior of \cee commands in math environments
+  # but the redefinitions in chemformula are too deep to make this viable
+  # push(@MATHTEXTCMDLIST,'cee');
+}
+
+
+my ( $citpat);
 
 if ( defined $packages{"apacite"}  ) {
-  print STDERR "DEBUG apacite citation commands\n"  if $debug;
-  $citpatsafe=qr/^(?:mask)?(?:full|short)?cite(?:A|author|year)?(?:NP)?$/;
+  print STDERR "apacite package detected.\n" if $verbose ;
   $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);
+if ( ! $ulem ) {
+  # modes not using ulem: citation is safe
+  push (@SAFECMDLIST, $citpat);
 } else {
   ### Experimental: disable text and emph commands
-  push (@SAFECMDLIST, $citpatsafe) unless $disablecitmark;
   push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
   # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
+  push(@MBOXCMDLIST,$citpat) unless $disablecitmark;
   if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
     # remove \cite command again from list of safe commands
-    pop @SAFECMDLIST;
+    pop @MBOXCMDLIST;
     # 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 $enablecitmark ; # as above for explicit selection
+push(@MBOXCMDLIST,$citpat) if $enablecitmark ;
 
-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*';
 }
 
+# add commands in MBOXCMDLIST to SAFECMDLIST
+foreach $mboxcmd ( @MBOXCMDLIST ) {
+  init_regex_arr_ext(\@SAFECMDLIST, $mboxcmd);
+}
+
+
+
 print STDERR "Preprocessing body.  " if $verbose;
-my ($oldleadin,$newleadin)=preprocess($oldbody,$newbody);
+preprocess($oldbody,$newbody);
 
 
 # run difference algorithm
@@ -696,7 +803,7 @@ if (defined($visiblelabel)) {
   $diffbo = "\\begin{verbatim}LATEXDIFF comparison\nOld: $oldlabel\nNew: $newlabel\\end{verbatim}\n$diffbo"   ;
 }
 
-$diffall .= "$newleadin$diffbo" ;
+$diffall .= "$diffbo" ;
 $diffall .= "\\end{document}$newpost" if length $newpreamble ;
 if ( lc($encoding) ne "utf8" && lc($encoding) ne "ascii" ) {
   print STDERR "Encoding output file to $encoding\n" if $verbose;
@@ -758,22 +865,43 @@ sub read_file_with_encoding {
   return $output;
 }
 
-# %packages=list_packages(@preamble)
+## %packages=list_packages(@preamble)
+## 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)=@_;
+#  my %packages=();
+#  foreach $line ( @preamble ) {
+#    # get rid of comments
+#    $line=~s/(?<!\\)%.*$// ;
+#    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
+##      print STDERR "Found something: |$line|\n" if $debug;
+#      if (defined($1)) {
+#	$packages{$2}=$1;
+#      } else {
+#	$packages{$2}="";
+#      }
+#    }
+#  }
+#  return (%packages);
+#}
+
+
+# %packages=list_packages($preamble)
 # 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)=@_;
+  my ($preamble)=@_;
   my %packages=();
-  foreach $line ( @preamble ) {
-    # get rid of comments
-    $line=~s/(?<!\\)%.*$// ;
-    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
-#      print STDERR "Found something: |$line|\n";
-      if (defined($1)) {
-	$packages{$2}=$1;
-      } else {
-	$packages{$2}="";
-      }
+
+  # remove comments 
+  $preamble=~s/(?<!\\)%.*$//mg ;
+
+  while ( $preamble =~  m/\\(?:documentclass|usepackage|RequirePackage)(?:\[($brat0)\])?\{(.*?)\}/gs ) {
+    if (defined($1)) {
+      $packages{$2}=$1;
+    } else {
+      $packages{$2}="";
     }
   }
   return (%packages);
@@ -859,6 +987,7 @@ sub flatten {
 
   # recursively replace \\input and \\include files
   $text=~s/(^(?:[^%\n]|\\%)*)\\input{(.*?)}|\\include{(${includeonly}(?:\.tex)?)}/{ 
+	    $begline=(defined($1)? $1 : "") ;
 	    $fname = $2 if defined($2) ;
 	    $fname = $3 if defined($3) ;
             #      # add tex extension unless there is a three letter extension already 
@@ -870,7 +999,6 @@ sub flatten {
             ###$replacement=read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
 	    $replacement=flatten(read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding), $preamble,$filename,$encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
 	    # \include always starts a new page; use explicit \newpage command to simulate this
-	    $begline=(defined($1)? $1 : "") ;
 	    $newpage=(defined($3)? " \\newpage " : "") ;
 	    "$begline$newpage$replacement$newpage";
           }/exgm;
@@ -887,19 +1015,17 @@ sub flatten {
   }/exgm;
   # replace subfile with contents (subfile package)
   $text=~s/(^(?:[^%\n]|\\%)*)\\subfile{(.*?)}/{ 
-	   $fname = $2; 
+           $begline=(defined($1)? $1 : "") ;
+     	   $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;
 
@@ -1024,10 +1150,10 @@ sub bodydiff {
 
   print STDERR "(",exetime()," s)\n","Pass 2: inserting DIF tokens and mark up.  " if $verbose;
   if ( $debug ) {
-    open(TOKENOLD,">","latexdiff.debug.tokenold2.tex");
+    open(TOKENOLD,">","latexdiff.debug.tokenold2");
     print TOKENOLD join("***\n",@oldwords);
     close(TOKENOLD);
-    open(TOKENNEW,">","latexdiff.debug.tokennew2.tex");
+    open(TOKENNEW,">","latexdiff.debug.tokennew2");
     print TOKENNEW join("***\n",@newwords);
     close(TOKENNEW);
   }
@@ -1045,10 +1171,15 @@ sub bodydiff {
 # Each element of words is either
 # a word (including trailing spaces and punctuation)
 # a latex command
+# if there is white space in the beginning return that as first token
 sub splitlatex {
-  my ($string) = @_ ;
+  my ($inputstring) = @_ ;
+  my $string=$inputstring ;
   # if input is empty, return empty list
   length($string)>0 or return ();
+  $string=~s/^(\s*)//s;
+  my $leadin=$1;
+  length($string)>0 or return ($leadin);
 
   my @retval=($string =~ m/$pat/osg);  
 
@@ -1086,6 +1217,7 @@ sub splitlatex {
     }
 
   }
+  unshift(@retval,$leadin) if (length($leadin)>0);
   return @retval;
 }
 
@@ -1135,7 +1267,7 @@ sub pass1 {
 #			print STDERR "Unchanged block $cnt, $last1,$last2 \n";
                         if ($cnt < $MINWORDSBLOCK 
 			    && $cnt==scalar (
-				     grep { /^$wpat/ || ( /^\\([\w\d\*]+)((?:\[$brat0\]|\{$pat6\})*)/o 
+				     grep { /^$wpat/ || ( /^\\((?:[`'^"~=.]|[\w\d@*]+))((?:\[$brat0\]|\{$pat6\})*)/o 
 							   && iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL) 
 							   && scalar(@dummy=split(" ",$2))<3 ) }
 					     @$block) )  {
@@ -1267,7 +1399,7 @@ sub extracttextblocks {
   for ($i=0;$i< scalar @$block;$i++) {
     ($token,$index)=@{ $block->[$i] };
     # store pure text blocks
-    if ($token =~ /$wpat/ ||  ( $token =~/^\\([\w\d\*]+)((?:${extraspace}\[$brat0\]${extraspace}|${extraspace}\{$pat6\})*)/o 
+    if ($token =~ /$wpat/ ||  ( $token =~/^\\((?:[`'^"~=.]|[\w\d@\*]+))((?:${extraspace}\[$brat0\]${extraspace}|${extraspace}\{$pat6\})*)/o 
 				&& iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL) 
 				&& !iscmd($1,\@TEXTCMDLIST,\@TEXTCMDEXCL))) {
       # we have text or a command which can be treated as text
@@ -1411,7 +1543,7 @@ sub pass2 {
 }
 
 # marktags($openmark,$closemark,$open,$close,$opencmd,$closecmd,$comment,\@block)
-# returns ($openmark,$open,$block,$close,$closemark) if @block only contains no commands (except white-listed ones),
+# returns ($openmark,$open,$block,$close,$closemark) if @block contains no commands (except white-listed ones),
 # braces, ampersands, or comments
 # mark comments with $comment
 # exclude all other exceptions from scope of open, close like this
@@ -1431,8 +1563,11 @@ sub marktags {
 
 # split this block to flatten out sequences joined in pass1
   @$block=splitlatex(join "",@$block);
+  ### print STDERR "DEBUG: marktags $openmark,$closemark,$open,$close,$opencmd,$closecmd,$comment\n" if $debug;
+  ### print STDERR "DEBUG: marktags blocksplit ",join("|",@$block),"\n" if $debug;
   foreach (@$block) {
     $word=$_; 
+    ### print STDERR "DEBUG MARKTAGS: |$word|\n" if $debug;
     if ( $word =~ s/^%/%$comment/ ) {
       # a comment
       if ($cmd==1) {
@@ -1442,16 +1577,25 @@ sub marktags {
       push (@$retval,$word); 
       next;
     }
+    if ( $word =~ m/^\s*$/ ) {
+      ### print STDERR "DEBUG MARKTAGS: whitespace detected |$word| cmdcom |$cmdcomment| |$opencmd|\n" if $debug;
+      # a sequence of white-space characters - this should only ever happen for the first element of block.
+      # in deleted block, omit, otherwise just copy it in 
+      if ( ! $cmdcomment) {   # ignore in deleted blocks
+	push(@$retval,$word);
+      }
+      next;
+    }
     if (! $noncomment) {
       push (@$retval,$openmark); 
       $noncomment=1;
     }
-    # negative lookahead pattern (?!) in second clause is put in to avoid mathcing \( .. \) patterns
+    # negative lookahead pattern (?!) in second clause is put in to avoid matching \( .. \) patterns
     # also note that second pattern will match \\
-    # Note: the second pattern should really be $word =~ /^\\(?!\()(\\|[\w*@]+)/, ie * replaced by +
-    # and then all commands \" \' etc declared safe. But as I don't have a complete list of one letter 
-    # commands, and nobody has complained so far, I will eave this as is
-    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\(?!\()(\\|[\w*@]*)/ &&  !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
+    ### print STDERR "DEBUG marktags: Considering word |$word|\n";
+    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)/ &&  !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
+      ###print STDERR "DEBUG MARKTAGS is a non-safe command ($1)\n" if $debug;
+      ###    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\([\w*@\\% ]+)/ && !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
       # word is a command or other significant token (not in SAFECMDLIST)
 	## same conditions as in subroutine extractcommand:
 	# check if token is an alphanumeric command sequence with at least one non-optional argument
@@ -1496,6 +1640,7 @@ sub marktags {
 	  # ""
 	  local @SAFECMDLIST=(".*"); 
 	  local @SAFECMDEXCL=('\\','\\\\',@UNSAFEMATHCMD);
+	  ### print STDERR "DEBUG: Command $command argtext ",join(",",@argtext),"\n" if $debug;
 	  push(@$retval,$command,marktags("","",$open,$close,"","",$comment,\@argtext)#@argtext
                        ,$closingbracket);
         } else {
@@ -1513,10 +1658,21 @@ sub marktags {
 	$cmd=1;
       }
     } else {
-      # just an ordinary word or word in SAFECMD
+      ###print STDERR "DEBUG MARKTAGS is an ordinary word or SAFECMD command \n" if $debug;
+      # just an ordinary word or command in SAFECMD
       push (@$retval,$open) if $cmd==-1 ;
       push (@$retval,$closecmd,$open) if $cmd==1 ;
-      push (@$retval,$word);
+      ###TODO:  check here if it is a command in MBOXCMD list, and surround it with \mbox{...}
+      ### $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)/ &&  iscmd($1,\@MBOXCMDLIST,\@MBOXCMDEXCL))
+      ### but actually this check has been carried out already so can simply check if word begins with backslash
+      if ( $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)(.*?)(\s*)$/s &&  iscmd($1,\@MBOXCMDLIST,\@MBOXCMDEXCL)) {
+	# $word is a safe command in MBOXCMDLIST
+	###print STDERR "DEBUG Mboxsafecmd detected:$word:\n" if $debug ;
+	push(@$retval,"\\mbox{$AUXCMD\n\\" . $1 . $2 . $3 ."}$AUXCMD\n" );
+      } else {
+	# $word is a normal word or a safe command (not in MBOXCMDLIST
+	push (@$retval,$word);
+      }
       $cmd=0;
     }
   }
@@ -1530,7 +1686,7 @@ sub marktags {
 # preprocess($string, ..)
 # carry out the following pre-processing steps for all arguments:
 # 1. Remove leading white-space
-#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
+#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE and \& to \AMPERSAND
 # #.   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
@@ -1551,13 +1707,11 @@ sub marktags {
 #     names or labels but it does not matter because they are converted back in the postprocessing step
 # Returns: leading white space removed in step 1
 sub preprocess {
-  my @leadin=() ;
   for (@_) { 
-    s/^(\s*)//s;
-    push(@leadin,$1);
     #    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
     s/(?<!\\)\\{/\\QLEFTBRACE /sg;
     s/(?<!\\)\\}/\\QRIGHTBRACE /sg;
+    s/(?<!\\)\\&/\\AMPERSAND /sg;
 # replace {,} in comments with \\CLEFTBRACE,\\CRIGHTBRACE
     1 while s/((?<!\\)%.*)\{(.*)$/$1\\CLEFTBRACE $2/mg ;
     1 while s/((?<!\\)%.*)\}(.*)$/$1\\CRIGHTBRACE $2/mg ;
@@ -1590,7 +1744,6 @@ sub preprocess {
     # add final token " STOP"
     $_ .= " STOP"
   }
-  return(@leadin);
 }
 
 #hashstring=tohash(\%hash,$string)
@@ -1674,7 +1827,7 @@ sub fromhash {
 # 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, \end,{,}  in comments
-#    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
+#    Change \QLEFTBRACE, \QRIGHTBRACE,\AMPERSAND to \{,\},\&
 #
 # Note have to manually synchronize substitution commands below and 
 # DIF.. command names in the header
@@ -1693,10 +1846,6 @@ sub postprocess {
     # Replace \RIGHTBRACE by }    
     s/\\RIGHTBRACE/}/g;
 
-    # change citation commands within comments to protect from processing
-    if ($CITECMD){
-      1 while s/(%.*)\\($CITECMD)/$1\\CITEDIF$2/m ;
-    }
     # Check all deleted blocks: where a deleted block contains a matching \begin and
     #    \end environment (these will be disabled by a %DIFDELCMD statements), enable
     #    these commands again (such that for example displayed math in a deleted equation
@@ -1789,18 +1938,6 @@ sub postprocess {
 	substr($delblock,$begin2,$len2)=$mathblock;
 	pos($delblock) = $begin2 + length($mathblock);
       }
-      if ($CITE2CMD) {
-	$delblock=~s/($DELCMDOPEN\s*\\($CITE2CMD)(.*)$DELCMDCLOSE)/
-	  # Replacement code 
-	  {my ($aux,$all);
-	   $aux=$all=$1;
-	   $aux=~s#\n?($DELCMDOPEN|$DELCMDCLOSE)##g;
-	   $all."$aux$AUXCMD\n";}/sge;
-      }
-      # or protect \cite commands with \mbox
-      if ($CITECMD) {
-	$delblock=~s/(\\($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 ( $MBOXINLINEMATH ) {
 	# note additional \newline after command is omitted from output if right at the end of deleted block (otherwise a spurious empty line is generated)
@@ -1826,14 +1963,6 @@ sub postprocess {
 	substr($addblock,$begin2,$len2)=$mathblock;
 	pos($addblock) = $begin2 + length($mathblock);
       }
-      if ($CITECMD) {
-	my $addblockbefore=$addblock;
-	#(?: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;
@@ -1937,10 +2066,6 @@ sub postprocess {
     }
     # 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 ( $CITECMD ) {
-      1 while s/(%.*)\\CITEDIF($CITECMD)/$1\\$2/mg ;
-    }
 #   Convert \begin{SQUAREBRACKET} \end{SQUAREBRACKET} into \[ \]
     s/\\end{SQUAREBRACKET}/\\\]/sg;
     s/\\begin{SQUAREBRACKET}/\\\[/sg;
@@ -1959,6 +2084,7 @@ sub postprocess {
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
     s/\\QLEFTBRACE /\\{/sg;
     s/\\QRIGHTBRACE /\\}/sg;
+    s/\\AMPERSAND /\\&/sg;
 
   return;
   }
@@ -2212,14 +2338,15 @@ format as new.tex but has all changes relative to old.tex marked up or commented
 --type=markupstyle
 -t markupstyle         Add code to preamble for selected markup style
                        Available styles: UNDERLINE CTRADITIONAL TRADITIONAL CFONT FONTSTRIKE INVISIBLE 
-                                         CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR
+                                         CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR BOLD
                        [ Default: UNDERLINE ]
 
 --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 LABEL
+                       Available styles: SAFE MARGINAL DVIPSCOL COLOR ZLABEL ONLYCHANGEDPAGE (LABEL)*
                        [ Default: SAFE ]
+                       * LABEL subtype is deprecated
 
 --floattype=markstyle
 -f markstyle           Add code to preamble for selected style which 
@@ -2294,6 +2421,16 @@ format as new.tex but has all changes relative to old.tex marked up or commented
                        context2 commands are completely disabled in deleted sections, including
                        their arguments.
 
+--exclude-mboxsafecmd=exclude-file
+--exclude-mboxsafecmd="cmd1,cmd2,..."
+--append-mboxsafecmd=append-file
+--append-mboxsafecmd="cmd1,cmd2,..."
+                       Define safe commands, which additionally need to be protected by encapsulating
+                       in an \\mbox{..}. This is sometimes needed to get around incompatibilities 
+                       between external packages and the ulem package, which is  used for highlighting
+                       in the default style UNDERLINE as well as CULINECHBAR CFONTSTRIKE
+                       
+
 
 --config var1=val1,var2=val2,...
 -c var1=val1,..        Set configuration variables.
@@ -2317,7 +2454,7 @@ 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 apacite
+                       endfloat hyperref amsmath apacite siunitx cleveref glossaries mhchem chemformula
                        [ Default: scan the preamble for \\usepackage commands to determine
                          loaded packages.]
 
@@ -2358,10 +2495,15 @@ Other configuration options:
                                This mode is most suitable, if only minor changes to equations are
                                expected, e.g. correction of typos. 
 
---disable-citation-markup  Suppress citation markup in styles using ulem (UNDERLINE, 
-                       FONTSTRIKE, CULINECHBAR)
---enable-citation-markup   Protect citation commands in changed sections with \\mbox command
-                       [i.e. use default behaviour for ulem package for other packages]
+--disable-citation-markup 
+--disable-auto-mbox    Suppress citation markup and markup of other vulnerable commands in styles 
+                       using ulem (UNDERLINE,FONTSTRIKE, CULINECHBAR)
+                       (the two options are identical and are simply aliases)
+
+--enable-citation-markup
+--enforce-auto-mbox    Protect citation commands and other vulnerable commands in changed sections 
+                       with \\mbox command, i.e. use default behaviour for ulem package for other packages
+                       (the two options are identical and are simply aliases)
 
 Miscelleneous options
 
@@ -2550,7 +2692,7 @@ C<\DIFadd> and C<\DIFdel> commands.
 Available styles: 
 
 C<UNDERLINE CTRADITIONAL TRADITIONAL CFONT FONTSTRIKE INVISIBLE 
-CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR>
+CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR BOLD>
 
 [ Default: C<UNDERLINE> ]
 
@@ -2560,9 +2702,10 @@ 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 LABEL>
+Available styles: C<SAFE MARGINAL COLOR DVIPSCOL  ZLABEL ONLYCHANGEDPAGE (LABEL)*>
 
 [ Default: C<SAFE> ]
+* Subtype C<LABEL> is deprecated
 
 =item B<--floattype=markstyle> or
 B<-f markstyle>
@@ -2616,7 +2759,8 @@ The following packages trigger special behaviour:
 
 =item C<amsmath> 
 
-Configuration variable amsmath is set to C<align*> (Default: C<eqnarray*>)
+Configuration variable MATHARRREPL is set to C<align*> (Default: C<eqnarray*>). (Note that many of the 
+amsmath array environments are already recognised by default as such)
 
 =item C<endfloat> 
 
@@ -2633,10 +2777,31 @@ errors).
 
 Redefine the commands recognised as citation commands.
 
+=item C<siunitx>
+
+Treat C<\SI> as equivalent to citation commands (i.e. protect with C<\mbox> if markup style uses ulem package.
+
+=item C<cleveref>
+
+Treat C<\cref,\Cref>, etc as equivalent to citation commands (i.e. protect with C<\mbox> if markup style uses ulem package.
+
+=item C<glossaries>
+
+Define most of the glossaries commands as safe, protecting them with \mbox'es where needed
+
+=item C<mhchem>
+
+Treat C<\ce> as a safe command, i.e. it will be highlighted (note that C<\cee> will not be highlighted in equations as this leads to processing errors)
+
+=item C<chemformula>
+
+Treat C<\ch> as a safe command outside equations, i.e. it will be highlighted (note that C<\ch> will not be highlighted in equations as this leads to processing errors)
+
+
 =back
 
-[ Default: scan the preamble for C<\\usepackage> commands to determine
-  loaded packages.]
+[ Default: scan the preamble for C<\usepackage> commands to determine
+  loaded packages. ]
 
 
 
@@ -2702,11 +2867,24 @@ argument is shown as deleted text.
 
 =item B<--append-context2cmd=append-file> or
 =item B<--append-context2cmd="cmd1,cmd2,...">
+
 As corresponding commands for context1.  The only difference is that
 context2 commands are completely disabled in deleted sections, including
 their arguments.
 
 
+=item B<--exclude-mboxsafecmd=exclude-file> or B<--exclude-mboxsafecmd="cmd1,cmd2,...">
+
+=item B<--append-mboxsafecmd=append-file> or B<--append-mboxsafecmd="cmd1,cmd2,...">
+
+Define safe commands, which additionally need to be protected by encapsulating
+in an \\mbox{..}. This is sometimes needed to get around incompatibilities 
+between external packages and the ulem package, which is  used for highlighting
+in the default style UNDERLINE as well as CULINECHBAR CFONTSTRIKE
+
+
+
+
 
 =item B<--config var1=val1,var2=val2,...> or B<-c var1=val1,..>
 
@@ -2791,14 +2969,17 @@ C<fine> or C<3>: Detect small change in equations and mark up at fine granularit
 This mode is most suitable, if only minor changes to equations are
 expected, e.g. correction of typos. 
 
-=item B<--disable-citation-markup>
+=item B<--disable-citation-markup> or B<--disable-auto-mbox>
 
-Suppress citation markup in styles using ulem (UNDERLINE, 
-FONTSTRIKE, CULINECHBAR)
+Suppress citation markup and markup of other vulnerable commands in styles 
+using ulem (UNDERLINE,FONTSTRIKE, CULINECHBAR)
+(the two options are identical and are simply aliases)
 
-=item B<--enable-citation-markup>
+=item B<--enable-citation-markup> or B<--enforce-auto-mbox>
 
-Protect citation commands in changed sections with \\mbox command [i.e. use default behaviour for ulem package for other packages]
+Protect citation commands and other vulnerable commands in changed sections 
+with C<\mbox> command, i.e. use default behaviour for ulem package for other packages
+(the two options are identical and are simply aliases)
 
 =back
 
@@ -2842,7 +3023,7 @@ Suppress inclusion of old and new file names as comment in output file
 
 =item B<--visble-label>
 
-Include old and new filenames (or labels set with --label option) as 
+Include old and new filenames (or labels set with C<--label> option) as 
 visible output.
 
 =item B<--flatten>
@@ -2924,6 +3105,10 @@ No mark up of text, but mark margins with changebars (Requires changebar package
 
 No visible markup (but generic markup commands will still be inserted.
 
+=item C<BOLD>
+
+Added text is set in bold face, discarded is not shown.
+
 =back
 
 =head2 Subtypes
@@ -2956,6 +3141,20 @@ that C<DVIPSCOL> only works with the dvips converter, e.g. not pdflatex.
 (it is recommeneded to use instead the main types to effect colored markup,
 although in some cases coloring with dvipscol can be more complete).
 
+
+=item C<ZLABEL>
+
+can be used to highlight only changed pages, but requires post-processing. It is recommend to not call this option manually but use C<latexdiff-vc> with C<--only-changes> option. Alternatively, use the script given within preamble of diff files made using this style.
+
+=item C<ONLYCHANGEDPAGE> 
+
+also highlights changed pages, without the need for post-processing, but might not work reliably if
+there is floating material (figures, tables).
+
+=item C<LABEL> 
+
+is similar to C<ZLABEL>, but does not need the zref package and works less reliably (deprecated).
+
 =back
 
 =head2 Float Types
@@ -3042,26 +3241,34 @@ C<|subsubsection|paragraph|subparagraph)>  ]
 
 =back
 
-=head1 COMMON PROBLEMS
+=head1 COMMON PROBLEMS AND FAQ
 
 =over 10
 
 =item Citations result in overfull boxes
 
 There is an incompatibility between the C<ulem> package, which C<latexdiff> uses for underlining and striking out in the UNDERLINE style,
-the default style. In order to be able to mark up citations properly, they are placed with an C<\mbox> command in post-processing. As mboxes
-cannot be broken across lines, this procedure frequently results in overfull boxes, possibly obscuring the content as it extends beyond the right margin. If this is a problem, you have two possibilities:
+the default style, and the way citations are generated. In order to be able to mark up citations properly, they are enclosed with an C<\mbox> 
+command. As mboxes cannot be broken across lines, this procedure frequently results in overfull boxes, possibly obscuring the content as it extends beyond the right margin.  The same occurs for some other packages (e.g., siunitx). If this is a problem, you have two possibilities.
 
-1. Use C<COLOR> or C<DVIPSCOL> subtype markup (option C<-s COLOR>): If this markup is chosen, then changed citations are no longer marked up
-with the wavy line (additions) or struck out (deletions), but are still highlighted in the appropriate color.
+1. Use C<CFONT> type markup (option C<-t CFONT>): If this markup is chosen, then changed citations are no longer marked up
+with the wavy line (additions) or struck out (deletions), but are still highlighted in the appropriate color, and deleted text is shown with a different font. Other styles not using the C<ulem> package will also work. 
 
 2. Choose option C<--disable-citation-markup> which turns off the marking up of citations: deleted citations are no longer shown, and
-added ctations are shown without markup. (This was the default behaviour of latexdiff at versions 0.6 and older)
+added citations are shown without markup. (This was the default behaviour of latexdiff at versions 0.6 and older)
+
+For custom packages you can define the commands which need to be protected by C<\mbox> with C<--append-mboxsafecmd> and C<--excludemboxsafecmd> options
+(submit your lists of command as feature request at github page to set the default behaviour of future versions, see section 6)
 
 =item Changes in complicated mathematical equations result in latex processing errors
 
 Try options C<--math-markup=whole>.   If even that fails, you can turn off mark up for equations with C<--math-markup=off>.
 
+=item How can I just show the pages 
+
+Use options -C<-s ZLABEL>  (some postprocessing required) or C<-s ONLYCHANGEDPAGE>. C<latexdiff-vc --ps|--pdf> with C<--only-changes> option takes care of
+the post-processing for you (requires zref packages).
+
 =back
 
 =head1 BUGS
@@ -3071,7 +3278,7 @@ 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 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>
+or send them to I<tilmann -- AT -- 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
 above, and whose differencing still does not result in error-free
@@ -3098,8 +3305,8 @@ I<latexdiff-fast> requires the I<diff> command to be present.
 
 =head1 AUTHOR
 
-Version 1.0.4
-Copyright (C) 2004-2012 Frederik Tilmann
+Version 1.1.0
+Copyright (C) 2004-2015 Frederik Tilmann
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License Version 3
@@ -3323,7 +3530,10 @@ min
 Pr
 sec
 sup
-[Hclbdruvt]
+[Hclbkdruvt]
+[`'^"~=.]
+_
+AMPERSAND
 (SUPER|SUB)SCRIPTNB
 (SUPER|SUB)SCRIPT
 PERCENTAGE
@@ -3364,12 +3574,12 @@ sqrt
 %%END TEXT COMMANDS 
 
 %%BEGIN CONTEXT1 COMMANDS
-% Regex matching commands with a text argument (leave out the \), which will fail out of context, but whose argument should be printed as plain text
+% Regex matching commands with a text argument (leave out the \), which will fail out of context. These commands behave like text commands, except when they occur in a deleted section, where they are disabled, but their argument is shown as deleted text.
 caption
 %%END CONTEXT1 COMMANDS 
 
 %%BEGIN CONTEXT2 COMMANDS
-% Regex matching commands with a text argument (leave out the \), which will fail out of context, but whose argument should be printed as plain text
+% Regex matching commands with a text argument (leave out the \), which will fail out of context.  As corresponding commands for context1.  The only difference is that context2 commands are completely disabled in deleted sections, including their arguments.
 title
 author
 date
@@ -3444,6 +3654,10 @@ institute
 \providecommand{\DIFdel}[1]{}
 %DIF END INVISIBLE PREAMBLE
 
+%DIF BOLD PREAMBLE
+\providecommand{\DIFadd}[1]{{\bf #1}}
+\providecommand{\DIFdel}[1]{}
+%DIF END BOLD PREAMBLE
 
 %% SUBTYPES (Markers for beginning and end of changed blocks)
 
@@ -3481,24 +3695,94 @@ institute
 
 %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)
+% (only works for simple documents with non-repeated page numbers, otherwise use ZLABEL)
+% pdflatex diff.tex
+% pdflatex diff.tex
+%pdftk diff.pdf cat \
+%`perl -lne '\
+% if (m/\\newlabel{DIFchg[b](\d*)}{{.*}{(.*)}}/) { $start{$1}=$2; print $2}\
+% if (m/\\newlabel{DIFchg[e](\d*)}{{.*}{(.*)}}/) { \
+%      if (defined($start{$1})) { \
+%         for ($j=$start{$1}; $j<=$2; $j++) {print "$j";}\
+%      } else { \
+%         print "$2"\
+%      }\
+% }' diff.aux \
+% | uniq \
+% | tr  \\n ' '` \
+% output diff-changedpages.pdf
+% To show only pages with changes (dvips/dvipdf)
+% dvips -pp `\
+% [ put here the perl script from above]
+% | uniq | tr -s \\n ','`
+\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}}
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}}
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}}
+%DIF END LABEL PREAMBLE
+
+%DIF ZLABEL PREAMBLE
+% To show only pages with changes (pdf) (external program pdftk needs to be installed)
+% (uses zref for reference to absolute 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
+%pdftk diff.pdf cat \
+%`perl -lne 'if (m/\\zref\@newlabel{DIFchgb(\d*)}{.*\\abspage{(\d*)}}/ ) { $start{$1}=$2; print $2 } \
+%  if (m/\\zref\@newlabel{DIFchge(\d*)}{.*\\abspage{(\d*)}}/) { \
+%      if (defined($start{$1})) { \
+%         for ($j=$start{$1}; $j<=$2; $j++) {print "$j";}\
+%      } else { \
+%         print "$2"\
+%      }\
+% }' diff.aux \
+% | uniq \
+% | tr  \\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}
+\usepackage[user,abspage]{zref}
 \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
+\providecommand{\DIFaddbegin}{\global\advance\DIFcounterb 1\relax\zlabel{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\zlabel{DIFchge\the\DIFcountere}}
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\zlabel{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\zlabel{DIFchge\the\DIFcountere}}
+%DIF END ZLABEL PREAMBLE
+
+%DIF ONLYCHANGEDPAGE PREAMBLE
+\RequirePackage{atbegshi}
+\RequirePackage{etoolbox}
+\RequirePackage{zref}
+% redefine label command to write immediately to aux file - page references will be lost
+\makeatletter \let\oldlabel\label% Store \label 
+\renewcommand{\label}[1]{% Update \label to write to the .aux immediately 
+\zref@wrapper@immediate{\oldlabel{#1}}} 
+\makeatother 
+\newbool{DIFkeeppage}
+\newbool{DIFchange}
+\boolfalse{DIFkeeppage}
+\boolfalse{DIFchange}
+\AtBeginShipout{%
+  \ifbool{DIFkeeppage}
+        {\global\boolfalse{DIFkeeppage}}  % True DIFkeeppage
+         {\ifbool{DIFchange}{\global\boolfalse{DIFkeeppage}}{\global\boolfalse{DIFkeeppage}\AtBeginShipoutDiscard}} % False DIFkeeppage
+}
+\providecommand{\DIFaddbegin}{\global\booltrue{DIFkeeppage}\global\booltrue{DIFchange}}
+\providecommand{\DIFaddend}{\global\booltrue{DIFkeeppage}\global\boolfalse{DIFchange}}
+\providecommand{\DIFdelbegin}{\global\booltrue{DIFkeeppage}\global\booltrue{DIFchange}}
+\providecommand{\DIFdelend}{\global\booltrue{DIFkeeppage}\global\boolfalse{DIFchange}}
+%DIF END ONLYCHANGEDPAGE PREAMBLE
+
 %% FLOAT TYPES 
 
 %DIF FLOATSAFE PREAMBLE
diff --git a/Master/texmf-dist/doc/support/latexdiff/latexdiff-fast b/Master/texmf-dist/doc/support/latexdiff/latexdiff-fast
index 22f2f8f0344..01638677113 100755
--- a/Master/texmf-dist/doc/support/latexdiff/latexdiff-fast
+++ b/Master/texmf-dist/doc/support/latexdiff/latexdiff-fast
@@ -23,6 +23,19 @@
 # Detailed usage information at the end of the file
 #
 # ToDo:
+#      DONE
+#
+# Version 1.1.0
+#    - treat diacritics (\",\', etc) as safe commands
+#    - treat \_ and \& correctly as safe commands, even if used without spacing to the next word
+#    - Add a BOLD markup type that sets added text in bold face (Contribution by Victor Zabalza via pull request )
+#    - add append-mboxsafecmd list option to be able to specify special safe commands which need to be surrounded by mbox to avoid breaking (mostly this is needed with ulem package)
+#    - support for siunitx and cleveref packages: protect \SI command in siunitx package and \cref,\Cref{range}{*} in cleveref packages (thanks to Stefan Pinnow for testing)
+#    - experimental support for chemformula, mhchem packages: define \ch and \ce in packages as safe (but not \ch,\cee in equation array environments) - these unfortunately will not be marked up (thanks to Stefan Pinnow for testing)
+#    - bug fix: packages identified correctly even if \usepackage command options extend over several lines (previously \usepackage command needed to be fully contained in one line)
+#    - new subtype ONLYCHANGEDPAGE outputs only changed pages (might not work well for floating material)
+#    - new subtype ZLABEL operates similarly to LABEL but uses absolute page numbers (needs zref package)
+#    - undocumented option --debug/--nodebug to override default setting for debug mode (Default: 0 for release version, 1: for development version
 #
 # 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)
@@ -673,8 +686,8 @@ my ($algodiffversion)=split(/ /,$Algorithm::Diff::VERSION);
 
 
 my ($versionstring)=<<EOF ;
-This is LATEXDIFF 1.0.4  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
-  (c) 2004-2014 F J Tilmann
+This is LATEXDIFF 1.1.0  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
+  (c) 2004-2015 F J Tilmann
 EOF
 
 # Configuration variables: these have to be visible from the subroutines
@@ -693,8 +706,6 @@ my $COUNTERCMD='(?:footnote|part|chapter|section|subsection|subsubsection|paragr
                                         # 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
 
@@ -741,6 +752,9 @@ my @MATHTEXTCMDEXCL=();  #
 # Note I need to declare this with "our" instead of "my" because later in the code I have to "local"ise these  
 our @SAFECMDLIST=();  # array containing patterns of safe commands (which do not break when in the argument of DIFadd or DIFDEL)
 our @SAFECMDEXCL=();
+my @MBOXCMDLIST=();   # patterns for commands which are in principle safe but which need to be surrounded by an \mbox
+my @MBOXCMDEXCL=();           # all the patterns in MBOXCMDLIST will be appended to SAFECMDLIST
+
 
 my ($i,$j,$l);
 my ($old,$new);
@@ -760,6 +774,7 @@ my ($type,$subtype,$floattype,$config,$preamblefile,$encoding,$nolabel,$visiblel
     $replacecontext2,$appendcontext2,
     $help,$verbose,$driver,$version,$ignorewarnings,
     $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug,$earlylatexdiffpreamble);  ###$disablemathmark,
+my ($mboxsafe);
 # MNEMNONICS for mathmarkup
 my $mathmarkup;
 use constant {
@@ -769,9 +784,11 @@ use constant {
   FINE => 3
 };
 
+my ($mboxcmd);
 
 my (@configlist,@labels,
     @appendsafelist,@excludesafelist,
+    @appendmboxsafelist,@excludemboxsafelist,
     @appendtextlist,@excludetextlist,
     @appendcontext1list,@appendcontext2list,
     @packagelist);
@@ -780,9 +797,6 @@ my ($assign,@config);
 # the optional arguments to the package are the values of the hash elements
 my ($pkg,%packages);
 # Defaults
-$type='UNDERLINE';
-$subtype='SAFE';
-$floattype='FLOATSAFE';
 $mathmarkup=COARSE;
 
 $verbose=0;
@@ -828,6 +842,8 @@ GetOptions('type|t=s' => \$type,
 	   'append-context1cmd=s' => \@appendcontext1list,
 	   'replace-context2cmd=s' => \$replacecontext2,
 	   'append-context2cmd=s' => \@appendcontext2list,
+	   'exclude-mboxsafecmd=s' => \@excludemboxsafelist,
+	   'append-mboxsafecmd=s' => \@appendmboxsafelist,
 	   'show-preamble' => \$showpreamble,
 	   'show-safecmd' => \$showsafe,
 	   'show-textcmd' => \$showtext,
@@ -836,14 +852,15 @@ GetOptions('type|t=s' => \$type,
            'packages=s' => \@packagelist,
 	   'allow-spaces' => \$allowspaces,
            'math-markup=s' => \$mathmarkup,
-           'enable-citation-markup' => \$enablecitmark,
-           'disable-citation-markup' => \$disablecitmark,
+           'enable-citation-markup|enforce-auto-mbox' => \$enablecitmark,
+           'disable-citation-markup|disable-auto-mbox' => \$disablecitmark,
 	   'verbose|V' => \$verbose,
 	   'ignore-warnings' => \$ignorewarnings,
 	   'driver=s'=> \$driver,
 	   'flatten' => \$flatten,
 	   'version' => \$version,
-	   'help|h|H' => \$help);
+	   'help|h|H' => \$help,
+	   'debug!' => \$debug );
 
 if ( $help ) {
   usage() ;
@@ -859,6 +876,14 @@ print STDERR $versionstring if $verbose;
 if (defined($showall)){
   $showpreamble=$showsafe=$showtext=$showconfig=1;
 }
+# Default types
+$type='UNDERLINE' unless defined($type);
+$subtype='SAFE' unless defined($subtype);
+# set floattype to IDENTICAL for LABEL and ONLYCHANGEDPAGE subtype, unless it has been set explicitly on the command line
+$floattype=($subtype eq 'LABEL' || $subtype eq 'ONLYCHANGEDPAGE') ? 'IDENTICAL' : 'FLOATSAFE' unless defined($floattype);
+if ( $subtype eq 'LABEL' ) {
+  print STDERR "Note that LABEL subtype is deprecated. If possible, use ZLABEL instead (requires zref package)";
+}
 
 if (defined($mathmarkup)) {
   $mathmarkup=~tr/a-z/A-Z/;
@@ -899,6 +924,15 @@ foreach $appendsafe ( @appendsafelist ) {
 foreach $excludesafe ( @excludesafelist ) {
   init_regex_arr_ext(\@SAFECMDEXCL, $excludesafe);
 }
+# setting up @MBOXCMDLIST and @MBOXCMDEXCL
+foreach $mboxsafe ( @appendmboxsafelist ) {
+  init_regex_arr_ext(\@MBOXCMDLIST, $mboxsafe);
+}
+foreach $mboxsafe ( @excludemboxsafelist ) {
+  init_regex_arr_ext(\@MBOXCMDEXCL, $mboxsafe);
+}
+
+
 
 # setting up @TEXTCMDLIST and @TEXTCMDEXCL
 if (defined($replacetext)) {
@@ -1057,18 +1091,19 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $mathpunct='[+=<>\-\|]';
   my $and = '&';
   my $coords= '[\-.,\s\d]*';
+# quoted underscore - this needs special treatment as perl treats _ as a letter (\w) but latex does not
+# such that a\_b is interpreted as a{\_}b by latex but a{\_b} by perl
+  my $quotedunderscore='\\\\_';
 # word: sequence of letters or accents followed by letter
   my $word='(?:[-\w\d*]|\\\\[\"\'\`~^][A-Za-z\*])+';
   my $cmdleftright='\\\\(?:left|right|[Bb]igg?[lrm]?|middle)\s*(?:[<>()\[\]|]|\\\\(?:[|{}]|\w+))';
-
   my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:<'.$abrat0.'>|\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
   my $backslashnl='\\\\\n';
   my $oneletcmd='\\\\.\*?(?:\['.$brat0.'\]|\{'. $pat6 . '\})*';
   my $math='\$(?:[^$]|\\\$)*?\$|\\\\[(](?:.|\n)*?\\\\[)]';
 ## the current maths command cannot cope with newline within the math expression
-
   my $comment='%.*?\n';
-  my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
+  my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$quotedunderscore|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
 
 # now we are done setting up and can start working   
 my ($oldfile, $newfile) = @ARGV;
@@ -1127,6 +1162,10 @@ if ($flatten) {
 
 
 my @auxlines;
+
+# boolean variab
+my ($ulem)=0;
+
 if ( length $oldpreamble && length $newpreamble ) {
   # pre-process preamble by looking for commands used in \maketitle (title, author, date etc commands) 
   # and marking up content with latexdiff markup
@@ -1140,22 +1179,19 @@ if ( length $oldpreamble && length $newpreamble ) {
   add_safe_commands($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" ;}
+  %packages=list_packages($newpreamble) unless %packages;
+  if ( %packages && $debug ) { my $key ; foreach $key (keys %packages) { print STDERR "DEBUG \\usepackage[",$packages{$key},"]{",$key,"}\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;
+    ###    $latexdiffpreamble .= '%DIF PREAMBLE EXTENSION ADDED BY LATEXDIFF FOR HYPERREF PACKAGE' . "\n";
+    ###    $latexdiffpreamble .= '\providecommand{\DIFadd}[1]{\texorpdfstring{\DIFaddtex{#1}}{#1}}' . "\n";
+    ###    $latexdiffpreamble .= '\providecommand{\DIFdel}[1]{\texorpdfstring{\DIFdeltex{#1}}{}}' . "\n";
+    ###    $latexdiffpreamble .= '%DIF END PREAMBLE EXTENSION ADDED BY LATEXDIFF FOR HYPERREF PACKAGE' . "\n";
   }
 
   print STDERR "Differencing preamble.\n" if $verbose;
@@ -1197,45 +1233,116 @@ elsif ( !length $oldpreamble && !length $newpreamble ) {
 # package documentation)
 # Use post-processing
 # and $packages{"apacite"}!~/natbibpapa/
-my ($citpat,$citpatsafe);
+
+$ulem = ($latexdiffpreamble =~ /\\RequirePackage(?:\[$brat0\])?\{ulem\}/ || defined $packages{"ulem"});
+
+
+if (defined $packages{"units"}  && $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;
+}
+
+if (defined $packages{"siunitx"} ) {
+  # protect SI command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between the ulem and siunitx package
+  print STDERR "siunitx package detected.\n" if $verbose ;
+  my $mboxcmds='SI,ang,numlist,numrange,SIlist,SIrange';
+  init_regex_arr_ext(\@SAFECMDLIST,'num,si');
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"cleveref"} ) {
+  # protect selected command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between ulem and cleveref package
+  print STDERR "cleveref package detected.\n" if $verbose ;
+  my $mboxcmds='[Cc]ref(?:range)?\*?,labelcref,(?:lc)?name[cC]refs?' ;
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"glossaries"} ) {
+  # protect selected command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between ulem and glossaries package 
+  print STDERR "glossaries package detected.\n" if $verbose ;
+  my $mboxcmds='[gG][lL][sS](?:|pl|disp|link|first|firstplural|desc|user[iv][iv]?[iv]?),[aA][cC][rR](?:long|longpl|full|fullpl),[aA][cC][lfp]?[lfp]?';
+  init_regex_arr_ext(\@SAFECMDLIST,'[gG][lL][sS](?:(?:entry)?(?:text|plural|name|symbol)|displaynumberlist|entryfirst|entryfirstplural|entrydesc|entrydescplural|entrysymbolplural|entryuser[iv][iv]?[iv]?|entrynumberlist|entrydisplaynumberlist|entrylong|entrylongpl|entryshort|entryshortpl|entryfull|entryfullpl),[gG]lossentry(?:name|desc|symbol),[aA][cC][rR](?:short|shortpl),[aA]csp?');
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"chemformula"} ) {
+  print STDERR "chemformula package detected.\n" if $verbose ;
+  init_regex_arr_ext(\@SAFECMDLIST,'ch');
+  push(@UNSAFEMATHCMD,'ch');
+  # The next command would be needed to allow highlighting the interior of \ch commands in math environments
+  # but the redefinitions in chemformula are too deep to make this viable
+  # push(@MATHTEXTCMDLIST,'ch');
+}
+
+if (defined $packages{"mhchem"} ) {
+  print STDERR "mhchem package detected.\n" if $verbose ;
+  init_regex_arr_ext(\@SAFECMDLIST,'ce');
+  push(@UNSAFEMATHCMD,'cee');
+  # The next command would be needed to allow highlighting the interior of \cee commands in math environments
+  # but the redefinitions in chemformula are too deep to make this viable
+  # push(@MATHTEXTCMDLIST,'cee');
+}
+
+
+my ( $citpat);
 
 if ( defined $packages{"apacite"}  ) {
-  print STDERR "DEBUG apacite citation commands\n"  if $debug;
-  $citpatsafe=qr/^(?:mask)?(?:full|short)?cite(?:A|author|year)?(?:NP)?$/;
+  print STDERR "apacite package detected.\n" if $verbose ;
   $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);
+if ( ! $ulem ) {
+  # modes not using ulem: citation is safe
+  push (@SAFECMDLIST, $citpat);
 } else {
   ### Experimental: disable text and emph commands
-  push (@SAFECMDLIST, $citpatsafe) unless $disablecitmark;
   push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
   # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
+  push(@MBOXCMDLIST,$citpat) unless $disablecitmark;
   if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
     # remove \cite command again from list of safe commands
-    pop @SAFECMDLIST;
+    pop @MBOXCMDLIST;
     # 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 $enablecitmark ; # as above for explicit selection
+push(@MBOXCMDLIST,$citpat) if $enablecitmark ;
 
-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*';
 }
 
+# add commands in MBOXCMDLIST to SAFECMDLIST
+foreach $mboxcmd ( @MBOXCMDLIST ) {
+  init_regex_arr_ext(\@SAFECMDLIST, $mboxcmd);
+}
+
+
+
 print STDERR "Preprocessing body.  " if $verbose;
-my ($oldleadin,$newleadin)=preprocess($oldbody,$newbody);
+preprocess($oldbody,$newbody);
 
 
 # run difference algorithm
@@ -1257,7 +1364,7 @@ if (defined($visiblelabel)) {
   $diffbo = "\\begin{verbatim}LATEXDIFF comparison\nOld: $oldlabel\nNew: $newlabel\\end{verbatim}\n$diffbo"   ;
 }
 
-$diffall .= "$newleadin$diffbo" ;
+$diffall .= "$diffbo" ;
 $diffall .= "\\end{document}$newpost" if length $newpreamble ;
 if ( lc($encoding) ne "utf8" && lc($encoding) ne "ascii" ) {
   print STDERR "Encoding output file to $encoding\n" if $verbose;
@@ -1319,22 +1426,43 @@ sub read_file_with_encoding {
   return $output;
 }
 
-# %packages=list_packages(@preamble)
+## %packages=list_packages(@preamble)
+## 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)=@_;
+#  my %packages=();
+#  foreach $line ( @preamble ) {
+#    # get rid of comments
+#    $line=~s/(?<!\\)%.*$// ;
+#    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
+##      print STDERR "Found something: |$line|\n" if $debug;
+#      if (defined($1)) {
+#	$packages{$2}=$1;
+#      } else {
+#	$packages{$2}="";
+#      }
+#    }
+#  }
+#  return (%packages);
+#}
+
+
+# %packages=list_packages($preamble)
 # 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)=@_;
+  my ($preamble)=@_;
   my %packages=();
-  foreach $line ( @preamble ) {
-    # get rid of comments
-    $line=~s/(?<!\\)%.*$// ;
-    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
-#      print STDERR "Found something: |$line|\n";
-      if (defined($1)) {
-	$packages{$2}=$1;
-      } else {
-	$packages{$2}="";
-      }
+
+  # remove comments 
+  $preamble=~s/(?<!\\)%.*$//mg ;
+
+  while ( $preamble =~  m/\\(?:documentclass|usepackage|RequirePackage)(?:\[($brat0)\])?\{(.*?)\}/gs ) {
+    if (defined($1)) {
+      $packages{$2}=$1;
+    } else {
+      $packages{$2}="";
     }
   }
   return (%packages);
@@ -1420,6 +1548,7 @@ sub flatten {
 
   # recursively replace \\input and \\include files
   $text=~s/(^(?:[^%\n]|\\%)*)\\input{(.*?)}|\\include{(${includeonly}(?:\.tex)?)}/{ 
+	    $begline=(defined($1)? $1 : "") ;
 	    $fname = $2 if defined($2) ;
 	    $fname = $3 if defined($3) ;
             #      # add tex extension unless there is a three letter extension already 
@@ -1431,7 +1560,6 @@ sub flatten {
             ###$replacement=read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
 	    $replacement=flatten(read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding), $preamble,$filename,$encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
 	    # \include always starts a new page; use explicit \newpage command to simulate this
-	    $begline=(defined($1)? $1 : "") ;
 	    $newpage=(defined($3)? " \\newpage " : "") ;
 	    "$begline$newpage$replacement$newpage";
           }/exgm;
@@ -1448,19 +1576,17 @@ sub flatten {
   }/exgm;
   # replace subfile with contents (subfile package)
   $text=~s/(^(?:[^%\n]|\\%)*)\\subfile{(.*?)}/{ 
-	   $fname = $2; 
+           $begline=(defined($1)? $1 : "") ;
+     	   $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;
 
@@ -1585,10 +1711,10 @@ sub bodydiff {
 
   print STDERR "(",exetime()," s)\n","Pass 2: inserting DIF tokens and mark up.  " if $verbose;
   if ( $debug ) {
-    open(TOKENOLD,">","latexdiff.debug.tokenold2.tex");
+    open(TOKENOLD,">","latexdiff.debug.tokenold2");
     print TOKENOLD join("***\n",@oldwords);
     close(TOKENOLD);
-    open(TOKENNEW,">","latexdiff.debug.tokennew2.tex");
+    open(TOKENNEW,">","latexdiff.debug.tokennew2");
     print TOKENNEW join("***\n",@newwords);
     close(TOKENNEW);
   }
@@ -1606,10 +1732,15 @@ sub bodydiff {
 # Each element of words is either
 # a word (including trailing spaces and punctuation)
 # a latex command
+# if there is white space in the beginning return that as first token
 sub splitlatex {
-  my ($string) = @_ ;
+  my ($inputstring) = @_ ;
+  my $string=$inputstring ;
   # if input is empty, return empty list
   length($string)>0 or return ();
+  $string=~s/^(\s*)//s;
+  my $leadin=$1;
+  length($string)>0 or return ($leadin);
 
   my @retval=($string =~ m/$pat/osg);  
 
@@ -1647,6 +1778,7 @@ sub splitlatex {
     }
 
   }
+  unshift(@retval,$leadin) if (length($leadin)>0);
   return @retval;
 }
 
@@ -1696,7 +1828,7 @@ sub pass1 {
 #			print STDERR "Unchanged block $cnt, $last1,$last2 \n";
                         if ($cnt < $MINWORDSBLOCK 
 			    && $cnt==scalar (
-				     grep { /^$wpat/ || ( /^\\([\w\d\*]+)((?:\[$brat0\]|\{$pat6\})*)/o 
+				     grep { /^$wpat/ || ( /^\\((?:[`'^"~=.]|[\w\d@*]+))((?:\[$brat0\]|\{$pat6\})*)/o 
 							   && iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL) 
 							   && scalar(@dummy=split(" ",$2))<3 ) }
 					     @$block) )  {
@@ -1828,7 +1960,7 @@ sub extracttextblocks {
   for ($i=0;$i< scalar @$block;$i++) {
     ($token,$index)=@{ $block->[$i] };
     # store pure text blocks
-    if ($token =~ /$wpat/ ||  ( $token =~/^\\([\w\d\*]+)((?:${extraspace}\[$brat0\]${extraspace}|${extraspace}\{$pat6\})*)/o 
+    if ($token =~ /$wpat/ ||  ( $token =~/^\\((?:[`'^"~=.]|[\w\d@\*]+))((?:${extraspace}\[$brat0\]${extraspace}|${extraspace}\{$pat6\})*)/o 
 				&& iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL) 
 				&& !iscmd($1,\@TEXTCMDLIST,\@TEXTCMDEXCL))) {
       # we have text or a command which can be treated as text
@@ -1972,7 +2104,7 @@ sub pass2 {
 }
 
 # marktags($openmark,$closemark,$open,$close,$opencmd,$closecmd,$comment,\@block)
-# returns ($openmark,$open,$block,$close,$closemark) if @block only contains no commands (except white-listed ones),
+# returns ($openmark,$open,$block,$close,$closemark) if @block contains no commands (except white-listed ones),
 # braces, ampersands, or comments
 # mark comments with $comment
 # exclude all other exceptions from scope of open, close like this
@@ -1992,8 +2124,11 @@ sub marktags {
 
 # split this block to flatten out sequences joined in pass1
   @$block=splitlatex(join "",@$block);
+  ### print STDERR "DEBUG: marktags $openmark,$closemark,$open,$close,$opencmd,$closecmd,$comment\n" if $debug;
+  ### print STDERR "DEBUG: marktags blocksplit ",join("|",@$block),"\n" if $debug;
   foreach (@$block) {
     $word=$_; 
+    ### print STDERR "DEBUG MARKTAGS: |$word|\n" if $debug;
     if ( $word =~ s/^%/%$comment/ ) {
       # a comment
       if ($cmd==1) {
@@ -2003,16 +2138,25 @@ sub marktags {
       push (@$retval,$word); 
       next;
     }
+    if ( $word =~ m/^\s*$/ ) {
+      ### print STDERR "DEBUG MARKTAGS: whitespace detected |$word| cmdcom |$cmdcomment| |$opencmd|\n" if $debug;
+      # a sequence of white-space characters - this should only ever happen for the first element of block.
+      # in deleted block, omit, otherwise just copy it in 
+      if ( ! $cmdcomment) {   # ignore in deleted blocks
+	push(@$retval,$word);
+      }
+      next;
+    }
     if (! $noncomment) {
       push (@$retval,$openmark); 
       $noncomment=1;
     }
-    # negative lookahead pattern (?!) in second clause is put in to avoid mathcing \( .. \) patterns
+    # negative lookahead pattern (?!) in second clause is put in to avoid matching \( .. \) patterns
     # also note that second pattern will match \\
-    # Note: the second pattern should really be $word =~ /^\\(?!\()(\\|[\w*@]+)/, ie * replaced by +
-    # and then all commands \" \' etc declared safe. But as I don't have a complete list of one letter 
-    # commands, and nobody has complained so far, I will eave this as is
-    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\(?!\()(\\|[\w*@]*)/ &&  !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
+    ### print STDERR "DEBUG marktags: Considering word |$word|\n";
+    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)/ &&  !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
+      ###print STDERR "DEBUG MARKTAGS is a non-safe command ($1)\n" if $debug;
+      ###    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\([\w*@\\% ]+)/ && !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
       # word is a command or other significant token (not in SAFECMDLIST)
 	## same conditions as in subroutine extractcommand:
 	# check if token is an alphanumeric command sequence with at least one non-optional argument
@@ -2057,6 +2201,7 @@ sub marktags {
 	  # ""
 	  local @SAFECMDLIST=(".*"); 
 	  local @SAFECMDEXCL=('\\','\\\\',@UNSAFEMATHCMD);
+	  ### print STDERR "DEBUG: Command $command argtext ",join(",",@argtext),"\n" if $debug;
 	  push(@$retval,$command,marktags("","",$open,$close,"","",$comment,\@argtext)#@argtext
                        ,$closingbracket);
         } else {
@@ -2074,10 +2219,21 @@ sub marktags {
 	$cmd=1;
       }
     } else {
-      # just an ordinary word or word in SAFECMD
+      ###print STDERR "DEBUG MARKTAGS is an ordinary word or SAFECMD command \n" if $debug;
+      # just an ordinary word or command in SAFECMD
       push (@$retval,$open) if $cmd==-1 ;
       push (@$retval,$closecmd,$open) if $cmd==1 ;
-      push (@$retval,$word);
+      ###TODO:  check here if it is a command in MBOXCMD list, and surround it with \mbox{...}
+      ### $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)/ &&  iscmd($1,\@MBOXCMDLIST,\@MBOXCMDEXCL))
+      ### but actually this check has been carried out already so can simply check if word begins with backslash
+      if ( $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)(.*?)(\s*)$/s &&  iscmd($1,\@MBOXCMDLIST,\@MBOXCMDEXCL)) {
+	# $word is a safe command in MBOXCMDLIST
+	###print STDERR "DEBUG Mboxsafecmd detected:$word:\n" if $debug ;
+	push(@$retval,"\\mbox{$AUXCMD\n\\" . $1 . $2 . $3 ."}$AUXCMD\n" );
+      } else {
+	# $word is a normal word or a safe command (not in MBOXCMDLIST
+	push (@$retval,$word);
+      }
       $cmd=0;
     }
   }
@@ -2091,7 +2247,7 @@ sub marktags {
 # preprocess($string, ..)
 # carry out the following pre-processing steps for all arguments:
 # 1. Remove leading white-space
-#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
+#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE and \& to \AMPERSAND
 # #.   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
@@ -2112,13 +2268,11 @@ sub marktags {
 #     names or labels but it does not matter because they are converted back in the postprocessing step
 # Returns: leading white space removed in step 1
 sub preprocess {
-  my @leadin=() ;
   for (@_) { 
-    s/^(\s*)//s;
-    push(@leadin,$1);
     #    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
     s/(?<!\\)\\{/\\QLEFTBRACE /sg;
     s/(?<!\\)\\}/\\QRIGHTBRACE /sg;
+    s/(?<!\\)\\&/\\AMPERSAND /sg;
 # replace {,} in comments with \\CLEFTBRACE,\\CRIGHTBRACE
     1 while s/((?<!\\)%.*)\{(.*)$/$1\\CLEFTBRACE $2/mg ;
     1 while s/((?<!\\)%.*)\}(.*)$/$1\\CRIGHTBRACE $2/mg ;
@@ -2151,7 +2305,6 @@ sub preprocess {
     # add final token " STOP"
     $_ .= " STOP"
   }
-  return(@leadin);
 }
 
 #hashstring=tohash(\%hash,$string)
@@ -2235,7 +2388,7 @@ sub fromhash {
 # 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, \end,{,}  in comments
-#    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
+#    Change \QLEFTBRACE, \QRIGHTBRACE,\AMPERSAND to \{,\},\&
 #
 # Note have to manually synchronize substitution commands below and 
 # DIF.. command names in the header
@@ -2254,10 +2407,6 @@ sub postprocess {
     # Replace \RIGHTBRACE by }    
     s/\\RIGHTBRACE/}/g;
 
-    # change citation commands within comments to protect from processing
-    if ($CITECMD){
-      1 while s/(%.*)\\($CITECMD)/$1\\CITEDIF$2/m ;
-    }
     # Check all deleted blocks: where a deleted block contains a matching \begin and
     #    \end environment (these will be disabled by a %DIFDELCMD statements), enable
     #    these commands again (such that for example displayed math in a deleted equation
@@ -2350,18 +2499,6 @@ sub postprocess {
 	substr($delblock,$begin2,$len2)=$mathblock;
 	pos($delblock) = $begin2 + length($mathblock);
       }
-      if ($CITE2CMD) {
-	$delblock=~s/($DELCMDOPEN\s*\\($CITE2CMD)(.*)$DELCMDCLOSE)/
-	  # Replacement code 
-	  {my ($aux,$all);
-	   $aux=$all=$1;
-	   $aux=~s#\n?($DELCMDOPEN|$DELCMDCLOSE)##g;
-	   $all."$aux$AUXCMD\n";}/sge;
-      }
-      # or protect \cite commands with \mbox
-      if ($CITECMD) {
-	$delblock=~s/(\\($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 ( $MBOXINLINEMATH ) {
 	# note additional \newline after command is omitted from output if right at the end of deleted block (otherwise a spurious empty line is generated)
@@ -2387,14 +2524,6 @@ sub postprocess {
 	substr($addblock,$begin2,$len2)=$mathblock;
 	pos($addblock) = $begin2 + length($mathblock);
       }
-      if ($CITECMD) {
-	my $addblockbefore=$addblock;
-	#(?: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;
@@ -2498,10 +2627,6 @@ sub postprocess {
     }
     # 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 ( $CITECMD ) {
-      1 while s/(%.*)\\CITEDIF($CITECMD)/$1\\$2/mg ;
-    }
 #   Convert \begin{SQUAREBRACKET} \end{SQUAREBRACKET} into \[ \]
     s/\\end{SQUAREBRACKET}/\\\]/sg;
     s/\\begin{SQUAREBRACKET}/\\\[/sg;
@@ -2520,6 +2645,7 @@ sub postprocess {
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
     s/\\QLEFTBRACE /\\{/sg;
     s/\\QRIGHTBRACE /\\}/sg;
+    s/\\AMPERSAND /\\&/sg;
 
   return;
   }
@@ -2773,14 +2899,15 @@ format as new.tex but has all changes relative to old.tex marked up or commented
 --type=markupstyle
 -t markupstyle         Add code to preamble for selected markup style
                        Available styles: UNDERLINE CTRADITIONAL TRADITIONAL CFONT FONTSTRIKE INVISIBLE 
-                                         CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR
+                                         CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR BOLD
                        [ Default: UNDERLINE ]
 
 --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 LABEL
+                       Available styles: SAFE MARGINAL DVIPSCOL COLOR ZLABEL ONLYCHANGEDPAGE (LABEL)*
                        [ Default: SAFE ]
+                       * LABEL subtype is deprecated
 
 --floattype=markstyle
 -f markstyle           Add code to preamble for selected style which 
@@ -2855,6 +2982,16 @@ format as new.tex but has all changes relative to old.tex marked up or commented
                        context2 commands are completely disabled in deleted sections, including
                        their arguments.
 
+--exclude-mboxsafecmd=exclude-file
+--exclude-mboxsafecmd="cmd1,cmd2,..."
+--append-mboxsafecmd=append-file
+--append-mboxsafecmd="cmd1,cmd2,..."
+                       Define safe commands, which additionally need to be protected by encapsulating
+                       in an \\mbox{..}. This is sometimes needed to get around incompatibilities 
+                       between external packages and the ulem package, which is  used for highlighting
+                       in the default style UNDERLINE as well as CULINECHBAR CFONTSTRIKE
+                       
+
 
 --config var1=val1,var2=val2,...
 -c var1=val1,..        Set configuration variables.
@@ -2878,7 +3015,7 @@ 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 apacite
+                       endfloat hyperref amsmath apacite siunitx cleveref glossaries mhchem chemformula
                        [ Default: scan the preamble for \\usepackage commands to determine
                          loaded packages.]
 
@@ -2919,10 +3056,15 @@ Other configuration options:
                                This mode is most suitable, if only minor changes to equations are
                                expected, e.g. correction of typos. 
 
---disable-citation-markup  Suppress citation markup in styles using ulem (UNDERLINE, 
-                       FONTSTRIKE, CULINECHBAR)
---enable-citation-markup   Protect citation commands in changed sections with \\mbox command
-                       [i.e. use default behaviour for ulem package for other packages]
+--disable-citation-markup 
+--disable-auto-mbox    Suppress citation markup and markup of other vulnerable commands in styles 
+                       using ulem (UNDERLINE,FONTSTRIKE, CULINECHBAR)
+                       (the two options are identical and are simply aliases)
+
+--enable-citation-markup
+--enforce-auto-mbox    Protect citation commands and other vulnerable commands in changed sections 
+                       with \\mbox command, i.e. use default behaviour for ulem package for other packages
+                       (the two options are identical and are simply aliases)
 
 Miscelleneous options
 
@@ -3111,7 +3253,7 @@ C<\DIFadd> and C<\DIFdel> commands.
 Available styles: 
 
 C<UNDERLINE CTRADITIONAL TRADITIONAL CFONT FONTSTRIKE INVISIBLE 
-CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR>
+CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR BOLD>
 
 [ Default: C<UNDERLINE> ]
 
@@ -3121,9 +3263,10 @@ 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 LABEL>
+Available styles: C<SAFE MARGINAL COLOR DVIPSCOL  ZLABEL ONLYCHANGEDPAGE (LABEL)*>
 
 [ Default: C<SAFE> ]
+* Subtype C<LABEL> is deprecated
 
 =item B<--floattype=markstyle> or
 B<-f markstyle>
@@ -3177,7 +3320,8 @@ The following packages trigger special behaviour:
 
 =item C<amsmath> 
 
-Configuration variable amsmath is set to C<align*> (Default: C<eqnarray*>)
+Configuration variable MATHARRREPL is set to C<align*> (Default: C<eqnarray*>). (Note that many of the 
+amsmath array environments are already recognised by default as such)
 
 =item C<endfloat> 
 
@@ -3194,10 +3338,31 @@ errors).
 
 Redefine the commands recognised as citation commands.
 
+=item C<siunitx>
+
+Treat C<\SI> as equivalent to citation commands (i.e. protect with C<\mbox> if markup style uses ulem package.
+
+=item C<cleveref>
+
+Treat C<\cref,\Cref>, etc as equivalent to citation commands (i.e. protect with C<\mbox> if markup style uses ulem package.
+
+=item C<glossaries>
+
+Define most of the glossaries commands as safe, protecting them with \mbox'es where needed
+
+=item C<mhchem>
+
+Treat C<\ce> as a safe command, i.e. it will be highlighted (note that C<\cee> will not be highlighted in equations as this leads to processing errors)
+
+=item C<chemformula>
+
+Treat C<\ch> as a safe command outside equations, i.e. it will be highlighted (note that C<\ch> will not be highlighted in equations as this leads to processing errors)
+
+
 =back
 
-[ Default: scan the preamble for C<\\usepackage> commands to determine
-  loaded packages.]
+[ Default: scan the preamble for C<\usepackage> commands to determine
+  loaded packages. ]
 
 
 
@@ -3263,11 +3428,24 @@ argument is shown as deleted text.
 
 =item B<--append-context2cmd=append-file> or
 =item B<--append-context2cmd="cmd1,cmd2,...">
+
 As corresponding commands for context1.  The only difference is that
 context2 commands are completely disabled in deleted sections, including
 their arguments.
 
 
+=item B<--exclude-mboxsafecmd=exclude-file> or B<--exclude-mboxsafecmd="cmd1,cmd2,...">
+
+=item B<--append-mboxsafecmd=append-file> or B<--append-mboxsafecmd="cmd1,cmd2,...">
+
+Define safe commands, which additionally need to be protected by encapsulating
+in an \\mbox{..}. This is sometimes needed to get around incompatibilities 
+between external packages and the ulem package, which is  used for highlighting
+in the default style UNDERLINE as well as CULINECHBAR CFONTSTRIKE
+
+
+
+
 
 =item B<--config var1=val1,var2=val2,...> or B<-c var1=val1,..>
 
@@ -3352,14 +3530,17 @@ C<fine> or C<3>: Detect small change in equations and mark up at fine granularit
 This mode is most suitable, if only minor changes to equations are
 expected, e.g. correction of typos. 
 
-=item B<--disable-citation-markup>
+=item B<--disable-citation-markup> or B<--disable-auto-mbox>
 
-Suppress citation markup in styles using ulem (UNDERLINE, 
-FONTSTRIKE, CULINECHBAR)
+Suppress citation markup and markup of other vulnerable commands in styles 
+using ulem (UNDERLINE,FONTSTRIKE, CULINECHBAR)
+(the two options are identical and are simply aliases)
 
-=item B<--enable-citation-markup>
+=item B<--enable-citation-markup> or B<--enforce-auto-mbox>
 
-Protect citation commands in changed sections with \\mbox command [i.e. use default behaviour for ulem package for other packages]
+Protect citation commands and other vulnerable commands in changed sections 
+with C<\mbox> command, i.e. use default behaviour for ulem package for other packages
+(the two options are identical and are simply aliases)
 
 =back
 
@@ -3403,7 +3584,7 @@ Suppress inclusion of old and new file names as comment in output file
 
 =item B<--visble-label>
 
-Include old and new filenames (or labels set with --label option) as 
+Include old and new filenames (or labels set with C<--label> option) as 
 visible output.
 
 =item B<--flatten>
@@ -3485,6 +3666,10 @@ No mark up of text, but mark margins with changebars (Requires changebar package
 
 No visible markup (but generic markup commands will still be inserted.
 
+=item C<BOLD>
+
+Added text is set in bold face, discarded is not shown.
+
 =back
 
 =head2 Subtypes
@@ -3517,6 +3702,20 @@ that C<DVIPSCOL> only works with the dvips converter, e.g. not pdflatex.
 (it is recommeneded to use instead the main types to effect colored markup,
 although in some cases coloring with dvipscol can be more complete).
 
+
+=item C<ZLABEL>
+
+can be used to highlight only changed pages, but requires post-processing. It is recommend to not call this option manually but use C<latexdiff-vc> with C<--only-changes> option. Alternatively, use the script given within preamble of diff files made using this style.
+
+=item C<ONLYCHANGEDPAGE> 
+
+also highlights changed pages, without the need for post-processing, but might not work reliably if
+there is floating material (figures, tables).
+
+=item C<LABEL> 
+
+is similar to C<ZLABEL>, but does not need the zref package and works less reliably (deprecated).
+
 =back
 
 =head2 Float Types
@@ -3603,26 +3802,34 @@ C<|subsubsection|paragraph|subparagraph)>  ]
 
 =back
 
-=head1 COMMON PROBLEMS
+=head1 COMMON PROBLEMS AND FAQ
 
 =over 10
 
 =item Citations result in overfull boxes
 
 There is an incompatibility between the C<ulem> package, which C<latexdiff> uses for underlining and striking out in the UNDERLINE style,
-the default style. In order to be able to mark up citations properly, they are placed with an C<\mbox> command in post-processing. As mboxes
-cannot be broken across lines, this procedure frequently results in overfull boxes, possibly obscuring the content as it extends beyond the right margin. If this is a problem, you have two possibilities:
+the default style, and the way citations are generated. In order to be able to mark up citations properly, they are enclosed with an C<\mbox> 
+command. As mboxes cannot be broken across lines, this procedure frequently results in overfull boxes, possibly obscuring the content as it extends beyond the right margin.  The same occurs for some other packages (e.g., siunitx). If this is a problem, you have two possibilities.
 
-1. Use C<COLOR> or C<DVIPSCOL> subtype markup (option C<-s COLOR>): If this markup is chosen, then changed citations are no longer marked up
-with the wavy line (additions) or struck out (deletions), but are still highlighted in the appropriate color.
+1. Use C<CFONT> type markup (option C<-t CFONT>): If this markup is chosen, then changed citations are no longer marked up
+with the wavy line (additions) or struck out (deletions), but are still highlighted in the appropriate color, and deleted text is shown with a different font. Other styles not using the C<ulem> package will also work. 
 
 2. Choose option C<--disable-citation-markup> which turns off the marking up of citations: deleted citations are no longer shown, and
-added ctations are shown without markup. (This was the default behaviour of latexdiff at versions 0.6 and older)
+added citations are shown without markup. (This was the default behaviour of latexdiff at versions 0.6 and older)
+
+For custom packages you can define the commands which need to be protected by C<\mbox> with C<--append-mboxsafecmd> and C<--excludemboxsafecmd> options
+(submit your lists of command as feature request at github page to set the default behaviour of future versions, see section 6)
 
 =item Changes in complicated mathematical equations result in latex processing errors
 
 Try options C<--math-markup=whole>.   If even that fails, you can turn off mark up for equations with C<--math-markup=off>.
 
+=item How can I just show the pages 
+
+Use options -C<-s ZLABEL>  (some postprocessing required) or C<-s ONLYCHANGEDPAGE>. C<latexdiff-vc --ps|--pdf> with C<--only-changes> option takes care of
+the post-processing for you (requires zref packages).
+
 =back
 
 =head1 BUGS
@@ -3632,7 +3839,7 @@ 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 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>
+or send them to I<tilmann -- AT -- 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
 above, and whose differencing still does not result in error-free
@@ -3659,8 +3866,8 @@ I<latexdiff-fast> requires the I<diff> command to be present.
 
 =head1 AUTHOR
 
-Version 1.0.4
-Copyright (C) 2004-2012 Frederik Tilmann
+Version 1.1.0
+Copyright (C) 2004-2015 Frederik Tilmann
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License Version 3
@@ -3884,7 +4091,10 @@ min
 Pr
 sec
 sup
-[Hclbdruvt]
+[Hclbkdruvt]
+[`'^"~=.]
+_
+AMPERSAND
 (SUPER|SUB)SCRIPTNB
 (SUPER|SUB)SCRIPT
 PERCENTAGE
@@ -3925,12 +4135,12 @@ sqrt
 %%END TEXT COMMANDS 
 
 %%BEGIN CONTEXT1 COMMANDS
-% Regex matching commands with a text argument (leave out the \), which will fail out of context, but whose argument should be printed as plain text
+% Regex matching commands with a text argument (leave out the \), which will fail out of context. These commands behave like text commands, except when they occur in a deleted section, where they are disabled, but their argument is shown as deleted text.
 caption
 %%END CONTEXT1 COMMANDS 
 
 %%BEGIN CONTEXT2 COMMANDS
-% Regex matching commands with a text argument (leave out the \), which will fail out of context, but whose argument should be printed as plain text
+% Regex matching commands with a text argument (leave out the \), which will fail out of context.  As corresponding commands for context1.  The only difference is that context2 commands are completely disabled in deleted sections, including their arguments.
 title
 author
 date
@@ -4005,6 +4215,10 @@ institute
 \providecommand{\DIFdel}[1]{}
 %DIF END INVISIBLE PREAMBLE
 
+%DIF BOLD PREAMBLE
+\providecommand{\DIFadd}[1]{{\bf #1}}
+\providecommand{\DIFdel}[1]{}
+%DIF END BOLD PREAMBLE
 
 %% SUBTYPES (Markers for beginning and end of changed blocks)
 
@@ -4042,24 +4256,94 @@ institute
 
 %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)
+% (only works for simple documents with non-repeated page numbers, otherwise use ZLABEL)
 % 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
+%pdftk diff.pdf cat \
+%`perl -lne '\
+% if (m/\\newlabel{DIFchg[b](\d*)}{{.*}{(.*)}}/) { $start{$1}=$2; print $2}\
+% if (m/\\newlabel{DIFchg[e](\d*)}{{.*}{(.*)}}/) { \
+%      if (defined($start{$1})) { \
+%         for ($j=$start{$1}; $j<=$2; $j++) {print "$j";}\
+%      } else { \
+%         print "$2"\
+%      }\
+% }' diff.aux \
+% | uniq \
+% | tr  \\n ' '` \
+% output diff-changedpages.pdf
+% To show only pages with changes (dvips/dvipdf)
+% dvips -pp `\
+% [ put here the perl script from above]
+% | uniq | tr -s \\n ','`
+\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}}
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}}
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}}
+%DIF END LABEL PREAMBLE
+
+%DIF ZLABEL PREAMBLE
+% To show only pages with changes (pdf) (external program pdftk needs to be installed)
+% (uses zref for reference to absolute page numbers)
+% pdflatex diff.tex
+% pdflatex diff.tex
+%pdftk diff.pdf cat \
+%`perl -lne 'if (m/\\zref\@newlabel{DIFchgb(\d*)}{.*\\abspage{(\d*)}}/ ) { $start{$1}=$2; print $2 } \
+%  if (m/\\zref\@newlabel{DIFchge(\d*)}{.*\\abspage{(\d*)}}/) { \
+%      if (defined($start{$1})) { \
+%         for ($j=$start{$1}; $j<=$2; $j++) {print "$j";}\
+%      } else { \
+%         print "$2"\
+%      }\
+% }' diff.aux \
+% | uniq \
+% | tr  \\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}
+\usepackage[user,abspage]{zref}
 \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
+\providecommand{\DIFaddbegin}{\global\advance\DIFcounterb 1\relax\zlabel{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\zlabel{DIFchge\the\DIFcountere}}
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\zlabel{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\zlabel{DIFchge\the\DIFcountere}}
+%DIF END ZLABEL PREAMBLE
+
+%DIF ONLYCHANGEDPAGE PREAMBLE
+\RequirePackage{atbegshi}
+\RequirePackage{etoolbox}
+\RequirePackage{zref}
+% redefine label command to write immediately to aux file - page references will be lost
+\makeatletter \let\oldlabel\label% Store \label 
+\renewcommand{\label}[1]{% Update \label to write to the .aux immediately 
+\zref@wrapper@immediate{\oldlabel{#1}}} 
+\makeatother 
+\newbool{DIFkeeppage}
+\newbool{DIFchange}
+\boolfalse{DIFkeeppage}
+\boolfalse{DIFchange}
+\AtBeginShipout{%
+  \ifbool{DIFkeeppage}
+        {\global\boolfalse{DIFkeeppage}}  % True DIFkeeppage
+         {\ifbool{DIFchange}{\global\boolfalse{DIFkeeppage}}{\global\boolfalse{DIFkeeppage}\AtBeginShipoutDiscard}} % False DIFkeeppage
+}
+\providecommand{\DIFaddbegin}{\global\booltrue{DIFkeeppage}\global\booltrue{DIFchange}}
+\providecommand{\DIFaddend}{\global\booltrue{DIFkeeppage}\global\boolfalse{DIFchange}}
+\providecommand{\DIFdelbegin}{\global\booltrue{DIFkeeppage}\global\booltrue{DIFchange}}
+\providecommand{\DIFdelend}{\global\booltrue{DIFkeeppage}\global\boolfalse{DIFchange}}
+%DIF END ONLYCHANGEDPAGE PREAMBLE
+
 %% FLOAT TYPES 
 
 %DIF FLOATSAFE PREAMBLE
diff --git a/Master/texmf-dist/scripts/latexdiff/latexdiff-vc.pl b/Master/texmf-dist/scripts/latexdiff/latexdiff-vc.pl
index d38fc146441..7d954c15ec2 100755
--- a/Master/texmf-dist/scripts/latexdiff/latexdiff-vc.pl
+++ b/Master/texmf-dist/scripts/latexdiff/latexdiff-vc.pl
@@ -9,7 +9,7 @@
 # CTAN page:          http://www.ctan.org/tex-archive/support/latexdiff
 #
 #
-#   Contributors: S Utcke, H Bruyninckx
+#   Contributors: S Utcke, H Bruyninckx, C Junghans
 #
 #    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
@@ -25,7 +25,12 @@
 #
 # Detailed usage information at the end of the file
 #
-# version 1.0.4alpha:
+# version 1.1.0:
+#
+#      - with option --flatten and version control option, checkout the whole tree into a temporary directory
+#        (use svn info + checkout ; git archive )
+#       - add option --only-changes to output only changed pages (in combination with --ps or --pdf option)
+# version 1.0.4:
 #	- [ Patch #3486 contributed by cbarbu] add additional compilation for styles using chbar + avoid pdf/postscripts repeat in the code
 # version 1.0.3: Bug fix: replace use of system('cp...') with File::Copy::copy (Patch contributed by D. Bremner)
 #                 Quotes around system call file arguments to allow filenames with spaces (Patch contributed by ssteve)
@@ -48,20 +53,20 @@ use strict ;
 use warnings ;
 
 my $versionstring=<<EOF ;
-This is LATEXDIFF-VC 1.0.4alpha
-  (c) 2005-2013 F J Tilmann
+This is LATEXDIFF-VC 1.1.0
+  (c) 2005-2015 F J Tilmann
 EOF
 
 
 # Option names
-my ($version,$help,$fast,$so,$postscript,$pdf,$force,$dir,$cvs,$rcs,$svn,$git,$diffcmd,$patchcmd,@revs);
+my ($version,$help,$fast,$so,$postscript,$pdf,$onlychanges,$flatten,$force,$dir,$cvs,$rcs,$svn,$git,$hg,$diffcmd,$patchcmd,@revs);
 # Preset Variables
 my $latexdiff="latexdiff"; # Program for making the comparison
 my $latexcmd="latex"; # latex compiler if not further identified
 my $vc="";
-my $tempdir=tempdir(CLEANUP => 1);
+my $tempdir=tempdir(CLEANUP => 1);   # generate a temp dir, which will automatically be deleted at program exit
 # Variables
-my ($file1,$file2,$diff,$diffbase,$answer,$options,$infile,$append,$dirname,$cwd);
+my ($file1,$file2,$diff,$diffbase,$rootdir,$answer,$options,$infile,$append,$dirname,$cwd);
 my (@files,@ldoptions,@tmpfiles,@ptmpfiles,@difffiles,$extracomp); # ,
 
 Getopt::Long::Configure('pass_through','bundling');
@@ -71,12 +76,15 @@ GetOptions('revision|r:s' => \@revs,
            'rcs' => \$rcs,
            'svn' => \$svn,
            'git' => \$git,
+           'hg' => \$hg,
            'dir|d:s' => \$dir,
 	   'fast' => \$fast,
 	   'so' => \$so,
            'postscript|ps' => \$postscript,
            'pdf' => \$pdf,
            'force' => \$force,
+	   'only-changes' => \$onlychanges,
+	   'flatten:s' => \$flatten,
            'version' => \$version,
 	   'help|h' => \$help);
 
@@ -102,15 +110,15 @@ if ( $cvs ) {
   $vc="CVS";
 }
 if ( $rcs ) {
-  die "Cannot specify more than one of --cvs, --rcs --svn or --git." if ($vc);
+  die "Cannot specify more than one of --cvs, --rcs, --svn --git or --hg." if ($vc);
   $vc="RCS";
 }
 if ( $svn ) {
-  die "Cannot specify more than one of --cvs, --rcs --svn or --git." if ($vc);
+  die "Cannot specify more than one of --cvs, --rcs, --svn --git or --hg." if ($vc);
   $vc="SVN";
 }
 if ( $git ) {
-  die "Cannot specify more than one of --cvs, --rcs, --svn or --git." if ($vc);
+  die "Cannot specify more than one of --cvs, --rcs, --svn --git or --hg." if ($vc);
   $vc="GIT";
 }
 
@@ -125,11 +133,17 @@ if ( defined($dir) && ( -f $dir || $dir =~ /^-/ ) ) {
   unshift @ARGV,$dir;
   $dir="";
 }
+# check whether the first file name or first passed-through option for latexdiff got misinterpreted as an option to an empty --flatten option
+if ( defined($flatten) && ( -f $flatten || $flatten =~ /^-/ ) ) {
+  unshift @ARGV,$flatten;
+  $flatten="";
+}
+
 
 #print "DEBUG: latexdiff-vc command line: ", join(" ",@ARGV), "\n"; 
 
 $file2=pop @ARGV;
-( defined($file2) && $file2 =~ /\.(tex|bbl)$/ ) or pod2usage("Must specify at least one tex or bbl file");
+( defined($file2) && $file2 =~ /\.(tex|bbl|flt)$/ ) or pod2usage("Must specify at least one tex, bbl or flt file");
 
 if (! $vc && scalar(@revs)>0 ) {
   # have to guess $vc
@@ -142,6 +156,8 @@ if (! $vc && scalar(@revs)>0 ) {
     $vc="SVN";
   } elsif ( $0 =~ /-git$/ ) {
     $vc="GIT";
+  } elsif ( $0 =~ /-hg$/ ) {
+    $vc="HG";
   } elsif ( -e "$file2,v" ) {
     print STDERR "Guess you are using RCS ...\n";
     $vc="RCS";
@@ -151,6 +167,9 @@ if (! $vc && scalar(@revs)>0 ) {
   } elsif ( -d ".git" ) {
     print STDERR "Guess you are using GIT ...\n";
     $vc="GIT";
+  } elsif ( -d ".hg" ) {
+    print STDERR "Guess you are using HG ...\n";
+    $vc="HG";
   } elsif ( -e "CVSROOT" || defined($ENV{"CVSROOT"}) ) {
     print STDERR "Guess you are using CVS ...\n";
     $vc="CVS";
@@ -181,6 +200,9 @@ if ( scalar(@revs)>0 ) {
     # alternatively:
     # $diffcmd  = "git diff ";
     # $patchcmd = "patch -R -p1";
+  } elsif ( $vc eq "HG" ) {
+    $diffcmd  = "hg diff -r";
+    $patchcmd = "patch -R -p1";
   } else {
     print STDERR "Unknown versioning system $vc \n";
     exit 10;
@@ -190,11 +212,11 @@ if ( scalar(@revs)>0 ) {
 
 # make file list (last arguments), initial arguments have to be passed to latexdiff
 # We assume an argument is a valid file rather than a latexdiff argument
-# if it has extension .tex or .bbl
+# if it has extension .tex, .bbl or .flt (output of flatex)
 
 @files=($file2);
 while( $file1=pop @ARGV ) {
-  if ( $file1 =~ /\.(tex|bbl)$/ ) {
+  if ( $file1 =~ /\.(tex|bbl|flt)$/ ) {
     # $file1 looks like a valid file name and is prepended to file list
     unshift @files, $file1 ;
   } else {
@@ -203,10 +225,38 @@ while( $file1=pop @ARGV ) {
   }
 }
 
+if ( defined($flatten) ) {
+  push @ldoptions, "--flatten" ;
+}
+
+# impose ZLABEL subtype if --only-changes option
+if ( $onlychanges ) {
+  push @ldoptions, "-s", "ZLABEL" ;
+}
+
 if ( scalar(@revs) == 0 ) {
   pod2usage("When -r option is not used, two .tex files (old and new) must be given on the command line") unless @files==2;
+  warn "Option -flatten should normally be combined with -r option (Results will probably not be as expected)" if $flatten;
     #  compare two files
   $file1=shift @files ;
+} else {
+  # revision control
+  if ( $flatten ) {
+    pod2usage("Only one root file must be given  if --flatten option is used with version control") if  @files != 1;
+    $tempdir='.' if ( $flatten eq "keep-intermediate" );
+    print "flatten tempdir |$tempdir|";
+    if ( $vc eq "SVN" ) {
+      my (@infoout)=`svn info`;
+      my (@urlline) = grep(/^URL:/, @infoout);
+      @urlline ==1 or die "Ambiguous output from svn info command."; 
+      ( $rootdir = $urlline[0] ) =~ s/URL:\s*// ;
+      chomp $rootdir;
+    } elsif ( $vc eq "GIT" || $vc eq "HG" ) {
+      # do nothing
+    } else {
+      die "--flatten option with revision control only possible with SVN, HG and GIT modes";
+    }
+  }
 }
 
 if ( scalar(@revs) == 2 ) {
@@ -231,29 +281,48 @@ if ( ($vc eq "SVN" || $vc eq "CVS") && scalar(@revs)) {
 
 
 # cycle through all files
-
 @difffiles=();
+
 while ( $infile=$file2=shift @files ) {
   print STDERR "Working on  $infile \n";
   if ( scalar(@revs) == 1 ) {
-    ($file1=$infile) =~ s/\.(tex|bbl)/-oldtmp-$$.$1/ ;
-    push @tmpfiles,$file1;
-    # compare file with previous version ($revs[0]="") or specified version
-    ### system("$diffcmd$revs[0] $infile| $patchcmd -o$file1") ;
-    if (system("$diffcmd$revs[0] \"$infile\" | $patchcmd -o\"$file1\"")==0  and -z $file1 ) {
-      # no differences detected, i.e. file is equal to current version
-      copy($infile,$file1) || die "copy($infile,$file1) failed: $!";
-    }
+    if ( defined($flatten) ) {
+       my $olddir=$tempdir . "/latexdiff-vc-$revs[0]";
+       print STDERR "Checking out old dir into: $olddir (rev: $revs[0])\n";
+       checkout_dir($revs[0],$olddir);
+       $file1=$olddir ."/".$infile;
+     } else {
+       ($file1=$infile) =~ s/\.(tex|bbl|flt)/-oldtmp-$$.$1/ ;
+       push @tmpfiles,$file1;
+       # compare file with previous version ($revs[0]="") or specified version
+       ### system("$diffcmd$revs[0] $infile| $patchcmd -o$file1") ;
+       if (system("$diffcmd$revs[0] \"$infile\" | $patchcmd -o\"$file1\"")==0  and -z $file1 ) {
+	 # no differences detected, i.e. file is equal to current version
+	 copy($infile,$file1) || die "copy($infile,$file1) failed: $!";
+       }
+     }
   } elsif ( scalar(@revs) == 2 ) {
-    ($file1=$infile) =~ s/\.(tex|bbl)/-oldtmp-$$.$1/ ;
-    $file2 =~ s/\.(tex|bbl)/-newtmp-$$.$1/ ;
-    push @tmpfiles,$file2;
-    if (system("$diffcmd$revs[1] $infile | $patchcmd -o$file2")==0 and -z $file2 ) {
-      copy($infile,$file2) || die "copy($infile,$file2) failed: $!";
+    if ( defined($flatten) ) {
+      my $olddir=$tempdir . "/latexdiff-vc-$revs[0]";
+      print STDERR "Checking out old dir into: $olddir (rev: $revs[0])\n";
+      checkout_dir($revs[0],$olddir);
+      $file1=$olddir ."/".$infile;
+
+      my $newdir=$tempdir . "/latexdiff-vc-$revs[1]";
+      print STDERR "Checking out new dir into: $newdir\n";
+      checkout_dir($revs[1],$newdir);
+      $file2=$newdir ."/".$infile;
+    } else {
+      ($file1=$infile) =~ s/\.(tex|bbl|flt)/-oldtmp-$$.$1/ ;
+      $file2 =~ s/\.(tex|bbl|flt)/-newtmp-$$.$1/ ;
+      push @tmpfiles,$file2;
+      if (system("$diffcmd$revs[1] $infile | $patchcmd -o$file2")==0 and -z $file2 ) {
+	copy($infile,$file2) || die "copy($infile,$file2) failed: $!";
+      }
+      if (system("$diffcmd$revs[0] $infile | $patchcmd -o$file1")==0 and -z $file1 ) {
+	copy($infile,$file1) || die "copy($infile,$file1) failed: $!";
+      };
     }
-    if (system("$diffcmd$revs[0] $infile | $patchcmd -o$file1")==0 and -z $file1 ) {
-       copy($infile,$file1) || die "copy($infile,$file1) failed: $!";
-    };
   }
 
   if ( -z $file1 || -z $file2) {
@@ -265,15 +334,16 @@ while ( $infile=$file2=shift @files ) {
   if ( defined($dir) ) {
     $diff="$dir/$infile" ; 
   } else {
-    ($diff=$infile) =~ s/\.(tex|bbl)$/$append.$1/ ;
+    ($diff=$infile) =~ s/\.(tex|bbl|flt)$/$append.$1/ ;
   }
+   
   # make directories if needed
   $dirname=dirname($diff) ;
   system("mkdir -p $dirname") unless ( -e $dirname );
 
   # Remaining options are passed to latexdiff
   $options = join(" ",@ldoptions);
-
+   
   if ( -e $diff && ! $force ) {
     print STDERR "OK to overwrite existing file $diff (y/n)? ";
     $answer = <STDIN> ;
@@ -287,7 +357,7 @@ while ( $infile=$file2=shift @files ) {
     print STDERR  "Something went wrong in $latexdiff. Deleting $diff and abort\n" ; unlink $diff ; exit(5) 
   };
   print "Generated difference file $diff\n";
-
+   
   if ( ( $postscript or $pdf ) and !( scalar(@revs) && greptex( qr/\\document(?:class|style)/ , $diff ) ) ) {
     # save filename for later processing if postscript or pdf conversion is requested and either two-file mode was used (scalar(@revs)==0) or the diff file contains documentclass statement (ie. is a root document)
     push @difffiles, $diff ;
@@ -334,12 +404,22 @@ foreach $diff ( @difffiles ) {
   if ( $postscript ) {
     my $dvi="$diffbase.dvi";
     my $ps="$diffbase.ps";
+    my $ppoption="";
 
-    system("dvips -o $ps $dvi");
+    if ( $onlychanges ) {
+      $ppoption="-pp ".join(",",findchangedpages("$diffbase.aux"));
+    }
+    system("dvips $ppoption -o $ps $dvi");
     push @ptmpfiles, "$diffbase.aux","$diffbase.log",$dvi ;
     print "Generated postscript file $ps\n";
   } 
   elsif ( $pdf ) {
+    if ( $onlychanges ) {
+      my @pages=findchangedpages("$diffbase.aux");
+      system ("pdftk \"$diffbase.pdf\" cat " . join(" ",@pages) . " output \"$diffbase-changedpage.pdf\"")==0 or 
+               die ("Could not execute <pdftk $diffbase.pdf cat " . join(" ",@pages) . " output $diffbase-changedpage.pdf> . Return code: $?");
+      move("$diffbase-changedpage.pdf","$diffbase.pdf");
+    }
     push @ptmpfiles, "$diffbase.aux","$diffbase.log";
   }
   }
@@ -347,7 +427,53 @@ foreach $diff ( @difffiles ) {
   chdir $cwd;
 }
 
+# findchangedpages($auxfile)
+# returns a list of the page numbers on which changes were marked with the ZLABEL subtype of latexdiff
+sub findchangedpages {
+  my ($auxfile) =@_;
+  my $j;
+  my (%pages);		# note that I use a hash with page numbers as keys and arbitrary values - this way I can use perl's built-in functions to get red of duplicates
+  my %start;
+  open(AUX,$auxfile) or die ("Could open aux file $auxfile . System error: $!");
+  while (<AUX>) {
+    if (m/\\zref\@newlabel{DIFchgb(\d*)}{.*\\abspage{(\d*)}}/ ) { 
+      $start{$1}=$2; $pages{$2}=1;
+    }
+    if (m/\\zref\@newlabel{DIFchge(\d*)}{.*\\abspage{(\d*)}}/) { 
+      if (defined($start{$1})) {
+	for ($j=$start{$1}; $j<=$2; $j++) {
+	  $pages{$j}=1;
+	}
+      } else {
+	$pages{$2}=1;
+      }
+    }
+  }
+  close(AUX);
+  # sort pages numerically (they should be sorted already; this is just to make sure
+  return(sort {$a <=> $b} keys(%pages));
+}
+
+# checkout_dir(rev,dirname)
+# checks out revision rev and stores it in dirname
+# uses global variables: $vc, $rootdir
+sub checkout_dir {
+  my ($rev,$dirname)=@_;
+
+  unless (-e $dirname) { mkdir $dirname or die "Cannot mkdir $dirname ." ;}
+  if ( $vc eq "SVN" ) {
+    system("svn checkout -r $rev $rootdir $dirname")==0 or die "Something went wrong in executing:  svn checkout -r $rev $rootdir $dirname";
+  } elsif ( $vc eq "GIT" ) {
+    system("git archive --format=tar $rev | ( cd $dirname ; tar -xf -)")==0 or die "Something went wrong in executing:  git archive --format=tar $rev | ( cd $dirname ; tar -xf -)";
+  } elsif ( $vc eq "HG" ) {
+    system("hg archive --type files -r $rev $dirname")==0 or die "Something went wrong in executing:  hg archive --type files -r $rev $dirname";
+  } else {
+    die "checkout_dir: only works with SVN, HG and GIT VCS system (selected: $vc)";
+  }
+}
+
 # greptex returns 1 if regex is not matched in filename
+# only the 25 first non-comment lines are scanned
 # 0 if there is a match
 sub greptex {
   my ($regex,$filename)=@_;
@@ -393,7 +519,7 @@ file in postscript or pdf format.
 
 =over 4
 
-=item B<--rcs>, B<--svn>, B<--cvs>, or B<--git>
+=item B<--rcs>, B<--svn>, B<--cvs>, B<--git> or B<--hg>
 
 Set the version system. 
 If no version system is specified, latexdiff-vc will venture a guess.
@@ -403,7 +529,7 @@ the respective versioning system. However, this default can still be overridden
 
 =item B<-r>, B<-r> F<rev> or B<--revision>, B<--revision=>F<rev>
 
-Choose revision (under RCS, CVS, SVN or GIT). One or two B<-r> options can be
+Choose revision (under RCS, CVS, SVN, GIT or HG). One or two B<-r> options can be
 specified, and they result in different behaviour:
 
 =over 4
@@ -440,6 +566,15 @@ to the
 original filename, creating the directory and subdirectories should they not exist already.  This is particularly useful in order to clone a
 complete directory hierarchy.  Optionally, a pathname F<path> can be specified, which is prepended instead of C<diff>.
 
+=item B<--flatten,--flatten=keep-intermediate>
+
+If combined with C<--git>, C<--svn> or C<--hg> option or the corresponding modes, check out the revisions to compare in a separate temporary directory, and then pass on option C<--flatten> to latexdiff. The directory in which C<latexdiff-vc> is invoked defines the subtree which will be checked out.
+Note that if additional files are needed which are not included in the flatten procedure (package files, included graphics), they need to be accessible in the current directory. If you use bibtex, it is recommended to include the C<.bbl> file in the version management.
+
+The generic usage of this function is : C<latexdiff-vc --flatten -r rev1 [-r rev2] master.tex> where master.tex is the project file containing the highest level of includes etc.
+
+With C<--flatten=keep-intermediate>, the intermediate revision snapshots are kept in the current directory (Default is to store them in a temporary directory and delete them after generating the diff file.)
+
 =item B<--fast> or B<--so>
 
 Use C<latexdiff-fast> or C<latexdiff-so>, respectively (instead of C<latexdiff>).
@@ -459,6 +594,12 @@ Generate pdf output from difference file using C<pdflatex>. This will
 run the sequence C<pdflatex; pdflatex> on the difference file, or
 C<pdflatex; bibtex; pdflatex; pdflatex> for files requiring bibtex.
 
+=item B<--only-changes>
+
+Post-process the output such that only pages with changes on them are displayed. This requires the use of subtype ZLABEL 
+in latexdiff, which will be set automatically, but any manually set -s option will be overruled (also requires zref package to 
+be installsed). (note that this option must be combined with --ps or --pdf to make sense)
+
 =item B<--force>
 
 Overwrite existing diff files without asking for confirmation. Default 
@@ -485,23 +626,24 @@ L<latexdiff>
 =head1 PORTABILITY
 
 I<latexdiff-vc> uses external commands and is therefore
-limited to Unix-like systems. It also requires the RCS version control
-system and latex to be installed on the system.  Modules from Perl 5.8
+limited to Unix-like systems. It also requires the a version control
+system and latex to be installed on the system to make use of all features.  Modules from Perl 5.8
 or higher are required.
 
 =head1 BUG REPORTING
 
 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-vc>
-(option C<--version>)
-.
+or send them to I<tilmann -- AT -- gfz-potsdam.de>.  Include the serial number of I<latexdiff-vc>
+(option C<--version>).
+
 =head1 AUTHOR
 
-Copyright (C) 2005,2012 Frederik Tilmann
+Copyright (C) 2005-2015 Frederik Tilmann
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License Version 3
-Contributors: S Utcke, H Bruyninckx
+Contributors: S Utcke, H Bruyninckx; some ideas have been inspired by git-latexdiff bash script.
+C. Junghans: Mercurial Support.
 
 =cut
 
diff --git a/Master/texmf-dist/scripts/latexdiff/latexdiff.pl b/Master/texmf-dist/scripts/latexdiff/latexdiff.pl
index 6cd69fd9353..171c24be7ae 100755
--- a/Master/texmf-dist/scripts/latexdiff/latexdiff.pl
+++ b/Master/texmf-dist/scripts/latexdiff/latexdiff.pl
@@ -23,6 +23,19 @@
 # Detailed usage information at the end of the file
 #
 # ToDo:
+#      DONE
+#
+# Version 1.1.0
+#    - treat diacritics (\",\', etc) as safe commands
+#    - treat \_ and \& correctly as safe commands, even if used without spacing to the next word
+#    - Add a BOLD markup type that sets added text in bold face (Contribution by Victor Zabalza via pull request )
+#    - add append-mboxsafecmd list option to be able to specify special safe commands which need to be surrounded by mbox to avoid breaking (mostly this is needed with ulem package)
+#    - support for siunitx and cleveref packages: protect \SI command in siunitx package and \cref,\Cref{range}{*} in cleveref packages (thanks to Stefan Pinnow for testing)
+#    - experimental support for chemformula, mhchem packages: define \ch and \ce in packages as safe (but not \ch,\cee in equation array environments) - these unfortunately will not be marked up (thanks to Stefan Pinnow for testing)
+#    - bug fix: packages identified correctly even if \usepackage command options extend over several lines (previously \usepackage command needed to be fully contained in one line)
+#    - new subtype ONLYCHANGEDPAGE outputs only changed pages (might not work well for floating material)
+#    - new subtype ZLABEL operates similarly to LABEL but uses absolute page numbers (needs zref package)
+#    - undocumented option --debug/--nodebug to override default setting for debug mode (Default: 0 for release version, 1: for development version
 #
 # 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)
@@ -569,8 +582,8 @@ my ($algodiffversion)=split(/ /,$Algorithm::Diff::VERSION);
 
 
 my ($versionstring)=<<EOF ;
-This is LATEXDIFF 1.0.4  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
-  (c) 2004-2014 F J Tilmann
+This is LATEXDIFF 1.1.0  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
+  (c) 2004-2015 F J Tilmann
 EOF
 
 # Configuration variables: these have to be visible from the subroutines
@@ -589,8 +602,6 @@ my $COUNTERCMD='(?:footnote|part|chapter|section|subsection|subsubsection|paragr
                                         # 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
 
@@ -637,6 +648,9 @@ my @MATHTEXTCMDEXCL=();  #
 # Note I need to declare this with "our" instead of "my" because later in the code I have to "local"ise these  
 our @SAFECMDLIST=();  # array containing patterns of safe commands (which do not break when in the argument of DIFadd or DIFDEL)
 our @SAFECMDEXCL=();
+my @MBOXCMDLIST=();   # patterns for commands which are in principle safe but which need to be surrounded by an \mbox
+my @MBOXCMDEXCL=();           # all the patterns in MBOXCMDLIST will be appended to SAFECMDLIST
+
 
 my ($i,$j,$l);
 my ($old,$new);
@@ -656,6 +670,7 @@ my ($type,$subtype,$floattype,$config,$preamblefile,$encoding,$nolabel,$visiblel
     $replacecontext2,$appendcontext2,
     $help,$verbose,$driver,$version,$ignorewarnings,
     $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug,$earlylatexdiffpreamble);  ###$disablemathmark,
+my ($mboxsafe);
 # MNEMNONICS for mathmarkup
 my $mathmarkup;
 use constant {
@@ -665,9 +680,11 @@ use constant {
   FINE => 3
 };
 
+my ($mboxcmd);
 
 my (@configlist,@labels,
     @appendsafelist,@excludesafelist,
+    @appendmboxsafelist,@excludemboxsafelist,
     @appendtextlist,@excludetextlist,
     @appendcontext1list,@appendcontext2list,
     @packagelist);
@@ -676,9 +693,6 @@ my ($assign,@config);
 # the optional arguments to the package are the values of the hash elements
 my ($pkg,%packages);
 # Defaults
-$type='UNDERLINE';
-$subtype='SAFE';
-$floattype='FLOATSAFE';
 $mathmarkup=COARSE;
 
 $verbose=0;
@@ -724,6 +738,8 @@ GetOptions('type|t=s' => \$type,
 	   'append-context1cmd=s' => \@appendcontext1list,
 	   'replace-context2cmd=s' => \$replacecontext2,
 	   'append-context2cmd=s' => \@appendcontext2list,
+	   'exclude-mboxsafecmd=s' => \@excludemboxsafelist,
+	   'append-mboxsafecmd=s' => \@appendmboxsafelist,
 	   'show-preamble' => \$showpreamble,
 	   'show-safecmd' => \$showsafe,
 	   'show-textcmd' => \$showtext,
@@ -732,14 +748,15 @@ GetOptions('type|t=s' => \$type,
            'packages=s' => \@packagelist,
 	   'allow-spaces' => \$allowspaces,
            'math-markup=s' => \$mathmarkup,
-           'enable-citation-markup' => \$enablecitmark,
-           'disable-citation-markup' => \$disablecitmark,
+           'enable-citation-markup|enforce-auto-mbox' => \$enablecitmark,
+           'disable-citation-markup|disable-auto-mbox' => \$disablecitmark,
 	   'verbose|V' => \$verbose,
 	   'ignore-warnings' => \$ignorewarnings,
 	   'driver=s'=> \$driver,
 	   'flatten' => \$flatten,
 	   'version' => \$version,
-	   'help|h|H' => \$help);
+	   'help|h|H' => \$help,
+	   'debug!' => \$debug );
 
 if ( $help ) {
   usage() ;
@@ -755,6 +772,14 @@ print STDERR $versionstring if $verbose;
 if (defined($showall)){
   $showpreamble=$showsafe=$showtext=$showconfig=1;
 }
+# Default types
+$type='UNDERLINE' unless defined($type);
+$subtype='SAFE' unless defined($subtype);
+# set floattype to IDENTICAL for LABEL and ONLYCHANGEDPAGE subtype, unless it has been set explicitly on the command line
+$floattype=($subtype eq 'LABEL' || $subtype eq 'ONLYCHANGEDPAGE') ? 'IDENTICAL' : 'FLOATSAFE' unless defined($floattype);
+if ( $subtype eq 'LABEL' ) {
+  print STDERR "Note that LABEL subtype is deprecated. If possible, use ZLABEL instead (requires zref package)";
+}
 
 if (defined($mathmarkup)) {
   $mathmarkup=~tr/a-z/A-Z/;
@@ -795,6 +820,15 @@ foreach $appendsafe ( @appendsafelist ) {
 foreach $excludesafe ( @excludesafelist ) {
   init_regex_arr_ext(\@SAFECMDEXCL, $excludesafe);
 }
+# setting up @MBOXCMDLIST and @MBOXCMDEXCL
+foreach $mboxsafe ( @appendmboxsafelist ) {
+  init_regex_arr_ext(\@MBOXCMDLIST, $mboxsafe);
+}
+foreach $mboxsafe ( @excludemboxsafelist ) {
+  init_regex_arr_ext(\@MBOXCMDEXCL, $mboxsafe);
+}
+
+
 
 # setting up @TEXTCMDLIST and @TEXTCMDEXCL
 if (defined($replacetext)) {
@@ -953,18 +987,19 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $mathpunct='[+=<>\-\|]';
   my $and = '&';
   my $coords= '[\-.,\s\d]*';
+# quoted underscore - this needs special treatment as perl treats _ as a letter (\w) but latex does not
+# such that a\_b is interpreted as a{\_}b by latex but a{\_b} by perl
+  my $quotedunderscore='\\\\_';
 # word: sequence of letters or accents followed by letter
   my $word='(?:[-\w\d*]|\\\\[\"\'\`~^][A-Za-z\*])+';
   my $cmdleftright='\\\\(?:left|right|[Bb]igg?[lrm]?|middle)\s*(?:[<>()\[\]|]|\\\\(?:[|{}]|\w+))';
-
   my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:<'.$abrat0.'>|\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
   my $backslashnl='\\\\\n';
   my $oneletcmd='\\\\.\*?(?:\['.$brat0.'\]|\{'. $pat6 . '\})*';
   my $math='\$(?:[^$]|\\\$)*?\$|\\\\[(](?:.|\n)*?\\\\[)]';
 ## the current maths command cannot cope with newline within the math expression
-
   my $comment='%.*?\n';
-  my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
+  my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$quotedunderscore|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
 
 # now we are done setting up and can start working   
 my ($oldfile, $newfile) = @ARGV;
@@ -1023,6 +1058,10 @@ if ($flatten) {
 
 
 my @auxlines;
+
+# boolean variab
+my ($ulem)=0;
+
 if ( length $oldpreamble && length $newpreamble ) {
   # pre-process preamble by looking for commands used in \maketitle (title, author, date etc commands) 
   # and marking up content with latexdiff markup
@@ -1036,22 +1075,19 @@ if ( length $oldpreamble && length $newpreamble ) {
   add_safe_commands($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" ;}
+  %packages=list_packages($newpreamble) unless %packages;
+  if ( %packages && $debug ) { my $key ; foreach $key (keys %packages) { print STDERR "DEBUG \\usepackage[",$packages{$key},"]{",$key,"}\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;
+    ###    $latexdiffpreamble .= '%DIF PREAMBLE EXTENSION ADDED BY LATEXDIFF FOR HYPERREF PACKAGE' . "\n";
+    ###    $latexdiffpreamble .= '\providecommand{\DIFadd}[1]{\texorpdfstring{\DIFaddtex{#1}}{#1}}' . "\n";
+    ###    $latexdiffpreamble .= '\providecommand{\DIFdel}[1]{\texorpdfstring{\DIFdeltex{#1}}{}}' . "\n";
+    ###    $latexdiffpreamble .= '%DIF END PREAMBLE EXTENSION ADDED BY LATEXDIFF FOR HYPERREF PACKAGE' . "\n";
   }
 
   print STDERR "Differencing preamble.\n" if $verbose;
@@ -1093,45 +1129,116 @@ elsif ( !length $oldpreamble && !length $newpreamble ) {
 # package documentation)
 # Use post-processing
 # and $packages{"apacite"}!~/natbibpapa/
-my ($citpat,$citpatsafe);
+
+$ulem = ($latexdiffpreamble =~ /\\RequirePackage(?:\[$brat0\])?\{ulem\}/ || defined $packages{"ulem"});
+
+
+if (defined $packages{"units"}  && $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;
+}
+
+if (defined $packages{"siunitx"} ) {
+  # protect SI command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between the ulem and siunitx package
+  print STDERR "siunitx package detected.\n" if $verbose ;
+  my $mboxcmds='SI,ang,numlist,numrange,SIlist,SIrange';
+  init_regex_arr_ext(\@SAFECMDLIST,'num,si');
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"cleveref"} ) {
+  # protect selected command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between ulem and cleveref package
+  print STDERR "cleveref package detected.\n" if $verbose ;
+  my $mboxcmds='[Cc]ref(?:range)?\*?,labelcref,(?:lc)?name[cC]refs?' ;
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"glossaries"} ) {
+  # protect selected command by surrounding them with an \mbox
+  # this is done to get around an incompatibility between ulem and glossaries package 
+  print STDERR "glossaries package detected.\n" if $verbose ;
+  my $mboxcmds='[gG][lL][sS](?:|pl|disp|link|first|firstplural|desc|user[iv][iv]?[iv]?),[aA][cC][rR](?:long|longpl|full|fullpl),[aA][cC][lfp]?[lfp]?';
+  init_regex_arr_ext(\@SAFECMDLIST,'[gG][lL][sS](?:(?:entry)?(?:text|plural|name|symbol)|displaynumberlist|entryfirst|entryfirstplural|entrydesc|entrydescplural|entrysymbolplural|entryuser[iv][iv]?[iv]?|entrynumberlist|entrydisplaynumberlist|entrylong|entrylongpl|entryshort|entryshortpl|entryfull|entryfullpl),[gG]lossentry(?:name|desc|symbol),[aA][cC][rR](?:short|shortpl),[aA]csp?');
+  if ( $enablecitmark || ( $ulem  && ! $disablecitmark )) {
+    init_regex_arr_ext(\@MBOXCMDLIST,$mboxcmds);
+  } else {
+    init_regex_arr_ext(\@SAFECMDLIST,$mboxcmds);
+  }
+}
+
+if (defined $packages{"chemformula"} ) {
+  print STDERR "chemformula package detected.\n" if $verbose ;
+  init_regex_arr_ext(\@SAFECMDLIST,'ch');
+  push(@UNSAFEMATHCMD,'ch');
+  # The next command would be needed to allow highlighting the interior of \ch commands in math environments
+  # but the redefinitions in chemformula are too deep to make this viable
+  # push(@MATHTEXTCMDLIST,'ch');
+}
+
+if (defined $packages{"mhchem"} ) {
+  print STDERR "mhchem package detected.\n" if $verbose ;
+  init_regex_arr_ext(\@SAFECMDLIST,'ce');
+  push(@UNSAFEMATHCMD,'cee');
+  # The next command would be needed to allow highlighting the interior of \cee commands in math environments
+  # but the redefinitions in chemformula are too deep to make this viable
+  # push(@MATHTEXTCMDLIST,'cee');
+}
+
+
+my ( $citpat);
 
 if ( defined $packages{"apacite"}  ) {
-  print STDERR "DEBUG apacite citation commands\n"  if $debug;
-  $citpatsafe=qr/^(?:mask)?(?:full|short)?cite(?:A|author|year)?(?:NP)?$/;
+  print STDERR "apacite package detected.\n" if $verbose ;
   $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);
+if ( ! $ulem ) {
+  # modes not using ulem: citation is safe
+  push (@SAFECMDLIST, $citpat);
 } else {
   ### Experimental: disable text and emph commands
-  push (@SAFECMDLIST, $citpatsafe) unless $disablecitmark;
   push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
   # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
+  push(@MBOXCMDLIST,$citpat) unless $disablecitmark;
   if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
     # remove \cite command again from list of safe commands
-    pop @SAFECMDLIST;
+    pop @MBOXCMDLIST;
     # 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 $enablecitmark ; # as above for explicit selection
+push(@MBOXCMDLIST,$citpat) if $enablecitmark ;
 
-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*';
 }
 
+# add commands in MBOXCMDLIST to SAFECMDLIST
+foreach $mboxcmd ( @MBOXCMDLIST ) {
+  init_regex_arr_ext(\@SAFECMDLIST, $mboxcmd);
+}
+
+
+
 print STDERR "Preprocessing body.  " if $verbose;
-my ($oldleadin,$newleadin)=preprocess($oldbody,$newbody);
+preprocess($oldbody,$newbody);
 
 
 # run difference algorithm
@@ -1153,7 +1260,7 @@ if (defined($visiblelabel)) {
   $diffbo = "\\begin{verbatim}LATEXDIFF comparison\nOld: $oldlabel\nNew: $newlabel\\end{verbatim}\n$diffbo"   ;
 }
 
-$diffall .= "$newleadin$diffbo" ;
+$diffall .= "$diffbo" ;
 $diffall .= "\\end{document}$newpost" if length $newpreamble ;
 if ( lc($encoding) ne "utf8" && lc($encoding) ne "ascii" ) {
   print STDERR "Encoding output file to $encoding\n" if $verbose;
@@ -1215,22 +1322,43 @@ sub read_file_with_encoding {
   return $output;
 }
 
-# %packages=list_packages(@preamble)
+## %packages=list_packages(@preamble)
+## 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)=@_;
+#  my %packages=();
+#  foreach $line ( @preamble ) {
+#    # get rid of comments
+#    $line=~s/(?<!\\)%.*$// ;
+#    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
+##      print STDERR "Found something: |$line|\n" if $debug;
+#      if (defined($1)) {
+#	$packages{$2}=$1;
+#      } else {
+#	$packages{$2}="";
+#      }
+#    }
+#  }
+#  return (%packages);
+#}
+
+
+# %packages=list_packages($preamble)
 # 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)=@_;
+  my ($preamble)=@_;
   my %packages=();
-  foreach $line ( @preamble ) {
-    # get rid of comments
-    $line=~s/(?<!\\)%.*$// ;
-    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
-#      print STDERR "Found something: |$line|\n";
-      if (defined($1)) {
-	$packages{$2}=$1;
-      } else {
-	$packages{$2}="";
-      }
+
+  # remove comments 
+  $preamble=~s/(?<!\\)%.*$//mg ;
+
+  while ( $preamble =~  m/\\(?:documentclass|usepackage|RequirePackage)(?:\[($brat0)\])?\{(.*?)\}/gs ) {
+    if (defined($1)) {
+      $packages{$2}=$1;
+    } else {
+      $packages{$2}="";
     }
   }
   return (%packages);
@@ -1316,6 +1444,7 @@ sub flatten {
 
   # recursively replace \\input and \\include files
   $text=~s/(^(?:[^%\n]|\\%)*)\\input{(.*?)}|\\include{(${includeonly}(?:\.tex)?)}/{ 
+	    $begline=(defined($1)? $1 : "") ;
 	    $fname = $2 if defined($2) ;
 	    $fname = $3 if defined($3) ;
             #      # add tex extension unless there is a three letter extension already 
@@ -1327,7 +1456,6 @@ sub flatten {
             ###$replacement=read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
 	    $replacement=flatten(read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding), $preamble,$filename,$encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
 	    # \include always starts a new page; use explicit \newpage command to simulate this
-	    $begline=(defined($1)? $1 : "") ;
 	    $newpage=(defined($3)? " \\newpage " : "") ;
 	    "$begline$newpage$replacement$newpage";
           }/exgm;
@@ -1344,19 +1472,17 @@ sub flatten {
   }/exgm;
   # replace subfile with contents (subfile package)
   $text=~s/(^(?:[^%\n]|\\%)*)\\subfile{(.*?)}/{ 
-	   $fname = $2; 
+           $begline=(defined($1)? $1 : "") ;
+     	   $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;
 
@@ -1481,10 +1607,10 @@ sub bodydiff {
 
   print STDERR "(",exetime()," s)\n","Pass 2: inserting DIF tokens and mark up.  " if $verbose;
   if ( $debug ) {
-    open(TOKENOLD,">","latexdiff.debug.tokenold2.tex");
+    open(TOKENOLD,">","latexdiff.debug.tokenold2");
     print TOKENOLD join("***\n",@oldwords);
     close(TOKENOLD);
-    open(TOKENNEW,">","latexdiff.debug.tokennew2.tex");
+    open(TOKENNEW,">","latexdiff.debug.tokennew2");
     print TOKENNEW join("***\n",@newwords);
     close(TOKENNEW);
   }
@@ -1502,10 +1628,15 @@ sub bodydiff {
 # Each element of words is either
 # a word (including trailing spaces and punctuation)
 # a latex command
+# if there is white space in the beginning return that as first token
 sub splitlatex {
-  my ($string) = @_ ;
+  my ($inputstring) = @_ ;
+  my $string=$inputstring ;
   # if input is empty, return empty list
   length($string)>0 or return ();
+  $string=~s/^(\s*)//s;
+  my $leadin=$1;
+  length($string)>0 or return ($leadin);
 
   my @retval=($string =~ m/$pat/osg);  
 
@@ -1543,6 +1674,7 @@ sub splitlatex {
     }
 
   }
+  unshift(@retval,$leadin) if (length($leadin)>0);
   return @retval;
 }
 
@@ -1592,7 +1724,7 @@ sub pass1 {
 #			print STDERR "Unchanged block $cnt, $last1,$last2 \n";
                         if ($cnt < $MINWORDSBLOCK 
 			    && $cnt==scalar (
-				     grep { /^$wpat/ || ( /^\\([\w\d\*]+)((?:\[$brat0\]|\{$pat6\})*)/o 
+				     grep { /^$wpat/ || ( /^\\((?:[`'^"~=.]|[\w\d@*]+))((?:\[$brat0\]|\{$pat6\})*)/o 
 							   && iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL) 
 							   && scalar(@dummy=split(" ",$2))<3 ) }
 					     @$block) )  {
@@ -1724,7 +1856,7 @@ sub extracttextblocks {
   for ($i=0;$i< scalar @$block;$i++) {
     ($token,$index)=@{ $block->[$i] };
     # store pure text blocks
-    if ($token =~ /$wpat/ ||  ( $token =~/^\\([\w\d\*]+)((?:${extraspace}\[$brat0\]${extraspace}|${extraspace}\{$pat6\})*)/o 
+    if ($token =~ /$wpat/ ||  ( $token =~/^\\((?:[`'^"~=.]|[\w\d@\*]+))((?:${extraspace}\[$brat0\]${extraspace}|${extraspace}\{$pat6\})*)/o 
 				&& iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL) 
 				&& !iscmd($1,\@TEXTCMDLIST,\@TEXTCMDEXCL))) {
       # we have text or a command which can be treated as text
@@ -1868,7 +2000,7 @@ sub pass2 {
 }
 
 # marktags($openmark,$closemark,$open,$close,$opencmd,$closecmd,$comment,\@block)
-# returns ($openmark,$open,$block,$close,$closemark) if @block only contains no commands (except white-listed ones),
+# returns ($openmark,$open,$block,$close,$closemark) if @block contains no commands (except white-listed ones),
 # braces, ampersands, or comments
 # mark comments with $comment
 # exclude all other exceptions from scope of open, close like this
@@ -1888,8 +2020,11 @@ sub marktags {
 
 # split this block to flatten out sequences joined in pass1
   @$block=splitlatex(join "",@$block);
+  ### print STDERR "DEBUG: marktags $openmark,$closemark,$open,$close,$opencmd,$closecmd,$comment\n" if $debug;
+  ### print STDERR "DEBUG: marktags blocksplit ",join("|",@$block),"\n" if $debug;
   foreach (@$block) {
     $word=$_; 
+    ### print STDERR "DEBUG MARKTAGS: |$word|\n" if $debug;
     if ( $word =~ s/^%/%$comment/ ) {
       # a comment
       if ($cmd==1) {
@@ -1899,16 +2034,25 @@ sub marktags {
       push (@$retval,$word); 
       next;
     }
+    if ( $word =~ m/^\s*$/ ) {
+      ### print STDERR "DEBUG MARKTAGS: whitespace detected |$word| cmdcom |$cmdcomment| |$opencmd|\n" if $debug;
+      # a sequence of white-space characters - this should only ever happen for the first element of block.
+      # in deleted block, omit, otherwise just copy it in 
+      if ( ! $cmdcomment) {   # ignore in deleted blocks
+	push(@$retval,$word);
+      }
+      next;
+    }
     if (! $noncomment) {
       push (@$retval,$openmark); 
       $noncomment=1;
     }
-    # negative lookahead pattern (?!) in second clause is put in to avoid mathcing \( .. \) patterns
+    # negative lookahead pattern (?!) in second clause is put in to avoid matching \( .. \) patterns
     # also note that second pattern will match \\
-    # Note: the second pattern should really be $word =~ /^\\(?!\()(\\|[\w*@]+)/, ie * replaced by +
-    # and then all commands \" \' etc declared safe. But as I don't have a complete list of one letter 
-    # commands, and nobody has complained so far, I will eave this as is
-    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\(?!\()(\\|[\w*@]*)/ &&  !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
+    ### print STDERR "DEBUG marktags: Considering word |$word|\n";
+    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)/ &&  !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
+      ###print STDERR "DEBUG MARKTAGS is a non-safe command ($1)\n" if $debug;
+      ###    if ( $word =~ /^[&{}\[\]]/ || ( $word =~ /^\\([\w*@\\% ]+)/ && !iscmd($1,\@SAFECMDLIST,\@SAFECMDEXCL)) ) {
       # word is a command or other significant token (not in SAFECMDLIST)
 	## same conditions as in subroutine extractcommand:
 	# check if token is an alphanumeric command sequence with at least one non-optional argument
@@ -1953,6 +2097,7 @@ sub marktags {
 	  # ""
 	  local @SAFECMDLIST=(".*"); 
 	  local @SAFECMDEXCL=('\\','\\\\',@UNSAFEMATHCMD);
+	  ### print STDERR "DEBUG: Command $command argtext ",join(",",@argtext),"\n" if $debug;
 	  push(@$retval,$command,marktags("","",$open,$close,"","",$comment,\@argtext)#@argtext
                        ,$closingbracket);
         } else {
@@ -1970,10 +2115,21 @@ sub marktags {
 	$cmd=1;
       }
     } else {
-      # just an ordinary word or word in SAFECMD
+      ###print STDERR "DEBUG MARKTAGS is an ordinary word or SAFECMD command \n" if $debug;
+      # just an ordinary word or command in SAFECMD
       push (@$retval,$open) if $cmd==-1 ;
       push (@$retval,$closecmd,$open) if $cmd==1 ;
-      push (@$retval,$word);
+      ###TODO:  check here if it is a command in MBOXCMD list, and surround it with \mbox{...}
+      ### $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)/ &&  iscmd($1,\@MBOXCMDLIST,\@MBOXCMDEXCL))
+      ### but actually this check has been carried out already so can simply check if word begins with backslash
+      if ( $word =~ /^\\(?!\()(\\|[`'^"~=.]|[\w*@]+)(.*?)(\s*)$/s &&  iscmd($1,\@MBOXCMDLIST,\@MBOXCMDEXCL)) {
+	# $word is a safe command in MBOXCMDLIST
+	###print STDERR "DEBUG Mboxsafecmd detected:$word:\n" if $debug ;
+	push(@$retval,"\\mbox{$AUXCMD\n\\" . $1 . $2 . $3 ."}$AUXCMD\n" );
+      } else {
+	# $word is a normal word or a safe command (not in MBOXCMDLIST
+	push (@$retval,$word);
+      }
       $cmd=0;
     }
   }
@@ -1987,7 +2143,7 @@ sub marktags {
 # preprocess($string, ..)
 # carry out the following pre-processing steps for all arguments:
 # 1. Remove leading white-space
-#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
+#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE and \& to \AMPERSAND
 # #.   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
@@ -2008,13 +2164,11 @@ sub marktags {
 #     names or labels but it does not matter because they are converted back in the postprocessing step
 # Returns: leading white space removed in step 1
 sub preprocess {
-  my @leadin=() ;
   for (@_) { 
-    s/^(\s*)//s;
-    push(@leadin,$1);
     #    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
     s/(?<!\\)\\{/\\QLEFTBRACE /sg;
     s/(?<!\\)\\}/\\QRIGHTBRACE /sg;
+    s/(?<!\\)\\&/\\AMPERSAND /sg;
 # replace {,} in comments with \\CLEFTBRACE,\\CRIGHTBRACE
     1 while s/((?<!\\)%.*)\{(.*)$/$1\\CLEFTBRACE $2/mg ;
     1 while s/((?<!\\)%.*)\}(.*)$/$1\\CRIGHTBRACE $2/mg ;
@@ -2047,7 +2201,6 @@ sub preprocess {
     # add final token " STOP"
     $_ .= " STOP"
   }
-  return(@leadin);
 }
 
 #hashstring=tohash(\%hash,$string)
@@ -2131,7 +2284,7 @@ sub fromhash {
 # 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, \end,{,}  in comments
-#    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
+#    Change \QLEFTBRACE, \QRIGHTBRACE,\AMPERSAND to \{,\},\&
 #
 # Note have to manually synchronize substitution commands below and 
 # DIF.. command names in the header
@@ -2150,10 +2303,6 @@ sub postprocess {
     # Replace \RIGHTBRACE by }    
     s/\\RIGHTBRACE/}/g;
 
-    # change citation commands within comments to protect from processing
-    if ($CITECMD){
-      1 while s/(%.*)\\($CITECMD)/$1\\CITEDIF$2/m ;
-    }
     # Check all deleted blocks: where a deleted block contains a matching \begin and
     #    \end environment (these will be disabled by a %DIFDELCMD statements), enable
     #    these commands again (such that for example displayed math in a deleted equation
@@ -2246,18 +2395,6 @@ sub postprocess {
 	substr($delblock,$begin2,$len2)=$mathblock;
 	pos($delblock) = $begin2 + length($mathblock);
       }
-      if ($CITE2CMD) {
-	$delblock=~s/($DELCMDOPEN\s*\\($CITE2CMD)(.*)$DELCMDCLOSE)/
-	  # Replacement code 
-	  {my ($aux,$all);
-	   $aux=$all=$1;
-	   $aux=~s#\n?($DELCMDOPEN|$DELCMDCLOSE)##g;
-	   $all."$aux$AUXCMD\n";}/sge;
-      }
-      # or protect \cite commands with \mbox
-      if ($CITECMD) {
-	$delblock=~s/(\\($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 ( $MBOXINLINEMATH ) {
 	# note additional \newline after command is omitted from output if right at the end of deleted block (otherwise a spurious empty line is generated)
@@ -2283,14 +2420,6 @@ sub postprocess {
 	substr($addblock,$begin2,$len2)=$mathblock;
 	pos($addblock) = $begin2 + length($mathblock);
       }
-      if ($CITECMD) {
-	my $addblockbefore=$addblock;
-	#(?: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;
@@ -2394,10 +2523,6 @@ sub postprocess {
     }
     # 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 ( $CITECMD ) {
-      1 while s/(%.*)\\CITEDIF($CITECMD)/$1\\$2/mg ;
-    }
 #   Convert \begin{SQUAREBRACKET} \end{SQUAREBRACKET} into \[ \]
     s/\\end{SQUAREBRACKET}/\\\]/sg;
     s/\\begin{SQUAREBRACKET}/\\\[/sg;
@@ -2416,6 +2541,7 @@ sub postprocess {
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
     s/\\QLEFTBRACE /\\{/sg;
     s/\\QRIGHTBRACE /\\}/sg;
+    s/\\AMPERSAND /\\&/sg;
 
   return;
   }
@@ -2669,14 +2795,15 @@ format as new.tex but has all changes relative to old.tex marked up or commented
 --type=markupstyle
 -t markupstyle         Add code to preamble for selected markup style
                        Available styles: UNDERLINE CTRADITIONAL TRADITIONAL CFONT FONTSTRIKE INVISIBLE 
-                                         CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR
+                                         CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR BOLD
                        [ Default: UNDERLINE ]
 
 --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 LABEL
+                       Available styles: SAFE MARGINAL DVIPSCOL COLOR ZLABEL ONLYCHANGEDPAGE (LABEL)*
                        [ Default: SAFE ]
+                       * LABEL subtype is deprecated
 
 --floattype=markstyle
 -f markstyle           Add code to preamble for selected style which 
@@ -2751,6 +2878,16 @@ format as new.tex but has all changes relative to old.tex marked up or commented
                        context2 commands are completely disabled in deleted sections, including
                        their arguments.
 
+--exclude-mboxsafecmd=exclude-file
+--exclude-mboxsafecmd="cmd1,cmd2,..."
+--append-mboxsafecmd=append-file
+--append-mboxsafecmd="cmd1,cmd2,..."
+                       Define safe commands, which additionally need to be protected by encapsulating
+                       in an \\mbox{..}. This is sometimes needed to get around incompatibilities 
+                       between external packages and the ulem package, which is  used for highlighting
+                       in the default style UNDERLINE as well as CULINECHBAR CFONTSTRIKE
+                       
+
 
 --config var1=val1,var2=val2,...
 -c var1=val1,..        Set configuration variables.
@@ -2774,7 +2911,7 @@ 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 apacite
+                       endfloat hyperref amsmath apacite siunitx cleveref glossaries mhchem chemformula
                        [ Default: scan the preamble for \\usepackage commands to determine
                          loaded packages.]
 
@@ -2815,10 +2952,15 @@ Other configuration options:
                                This mode is most suitable, if only minor changes to equations are
                                expected, e.g. correction of typos. 
 
---disable-citation-markup  Suppress citation markup in styles using ulem (UNDERLINE, 
-                       FONTSTRIKE, CULINECHBAR)
---enable-citation-markup   Protect citation commands in changed sections with \\mbox command
-                       [i.e. use default behaviour for ulem package for other packages]
+--disable-citation-markup 
+--disable-auto-mbox    Suppress citation markup and markup of other vulnerable commands in styles 
+                       using ulem (UNDERLINE,FONTSTRIKE, CULINECHBAR)
+                       (the two options are identical and are simply aliases)
+
+--enable-citation-markup
+--enforce-auto-mbox    Protect citation commands and other vulnerable commands in changed sections 
+                       with \\mbox command, i.e. use default behaviour for ulem package for other packages
+                       (the two options are identical and are simply aliases)
 
 Miscelleneous options
 
@@ -3007,7 +3149,7 @@ C<\DIFadd> and C<\DIFdel> commands.
 Available styles: 
 
 C<UNDERLINE CTRADITIONAL TRADITIONAL CFONT FONTSTRIKE INVISIBLE 
-CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR>
+CHANGEBAR CCHANGEBAR CULINECHBAR CFONTCBHBAR BOLD>
 
 [ Default: C<UNDERLINE> ]
 
@@ -3017,9 +3159,10 @@ 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 LABEL>
+Available styles: C<SAFE MARGINAL COLOR DVIPSCOL  ZLABEL ONLYCHANGEDPAGE (LABEL)*>
 
 [ Default: C<SAFE> ]
+* Subtype C<LABEL> is deprecated
 
 =item B<--floattype=markstyle> or
 B<-f markstyle>
@@ -3073,7 +3216,8 @@ The following packages trigger special behaviour:
 
 =item C<amsmath> 
 
-Configuration variable amsmath is set to C<align*> (Default: C<eqnarray*>)
+Configuration variable MATHARRREPL is set to C<align*> (Default: C<eqnarray*>). (Note that many of the 
+amsmath array environments are already recognised by default as such)
 
 =item C<endfloat> 
 
@@ -3090,10 +3234,31 @@ errors).
 
 Redefine the commands recognised as citation commands.
 
+=item C<siunitx>
+
+Treat C<\SI> as equivalent to citation commands (i.e. protect with C<\mbox> if markup style uses ulem package.
+
+=item C<cleveref>
+
+Treat C<\cref,\Cref>, etc as equivalent to citation commands (i.e. protect with C<\mbox> if markup style uses ulem package.
+
+=item C<glossaries>
+
+Define most of the glossaries commands as safe, protecting them with \mbox'es where needed
+
+=item C<mhchem>
+
+Treat C<\ce> as a safe command, i.e. it will be highlighted (note that C<\cee> will not be highlighted in equations as this leads to processing errors)
+
+=item C<chemformula>
+
+Treat C<\ch> as a safe command outside equations, i.e. it will be highlighted (note that C<\ch> will not be highlighted in equations as this leads to processing errors)
+
+
 =back
 
-[ Default: scan the preamble for C<\\usepackage> commands to determine
-  loaded packages.]
+[ Default: scan the preamble for C<\usepackage> commands to determine
+  loaded packages. ]
 
 
 
@@ -3159,11 +3324,24 @@ argument is shown as deleted text.
 
 =item B<--append-context2cmd=append-file> or
 =item B<--append-context2cmd="cmd1,cmd2,...">
+
 As corresponding commands for context1.  The only difference is that
 context2 commands are completely disabled in deleted sections, including
 their arguments.
 
 
+=item B<--exclude-mboxsafecmd=exclude-file> or B<--exclude-mboxsafecmd="cmd1,cmd2,...">
+
+=item B<--append-mboxsafecmd=append-file> or B<--append-mboxsafecmd="cmd1,cmd2,...">
+
+Define safe commands, which additionally need to be protected by encapsulating
+in an \\mbox{..}. This is sometimes needed to get around incompatibilities 
+between external packages and the ulem package, which is  used for highlighting
+in the default style UNDERLINE as well as CULINECHBAR CFONTSTRIKE
+
+
+
+
 
 =item B<--config var1=val1,var2=val2,...> or B<-c var1=val1,..>
 
@@ -3248,14 +3426,17 @@ C<fine> or C<3>: Detect small change in equations and mark up at fine granularit
 This mode is most suitable, if only minor changes to equations are
 expected, e.g. correction of typos. 
 
-=item B<--disable-citation-markup>
+=item B<--disable-citation-markup> or B<--disable-auto-mbox>
 
-Suppress citation markup in styles using ulem (UNDERLINE, 
-FONTSTRIKE, CULINECHBAR)
+Suppress citation markup and markup of other vulnerable commands in styles 
+using ulem (UNDERLINE,FONTSTRIKE, CULINECHBAR)
+(the two options are identical and are simply aliases)
 
-=item B<--enable-citation-markup>
+=item B<--enable-citation-markup> or B<--enforce-auto-mbox>
 
-Protect citation commands in changed sections with \\mbox command [i.e. use default behaviour for ulem package for other packages]
+Protect citation commands and other vulnerable commands in changed sections 
+with C<\mbox> command, i.e. use default behaviour for ulem package for other packages
+(the two options are identical and are simply aliases)
 
 =back
 
@@ -3299,7 +3480,7 @@ Suppress inclusion of old and new file names as comment in output file
 
 =item B<--visble-label>
 
-Include old and new filenames (or labels set with --label option) as 
+Include old and new filenames (or labels set with C<--label> option) as 
 visible output.
 
 =item B<--flatten>
@@ -3381,6 +3562,10 @@ No mark up of text, but mark margins with changebars (Requires changebar package
 
 No visible markup (but generic markup commands will still be inserted.
 
+=item C<BOLD>
+
+Added text is set in bold face, discarded is not shown.
+
 =back
 
 =head2 Subtypes
@@ -3413,6 +3598,20 @@ that C<DVIPSCOL> only works with the dvips converter, e.g. not pdflatex.
 (it is recommeneded to use instead the main types to effect colored markup,
 although in some cases coloring with dvipscol can be more complete).
 
+
+=item C<ZLABEL>
+
+can be used to highlight only changed pages, but requires post-processing. It is recommend to not call this option manually but use C<latexdiff-vc> with C<--only-changes> option. Alternatively, use the script given within preamble of diff files made using this style.
+
+=item C<ONLYCHANGEDPAGE> 
+
+also highlights changed pages, without the need for post-processing, but might not work reliably if
+there is floating material (figures, tables).
+
+=item C<LABEL> 
+
+is similar to C<ZLABEL>, but does not need the zref package and works less reliably (deprecated).
+
 =back
 
 =head2 Float Types
@@ -3499,26 +3698,34 @@ C<|subsubsection|paragraph|subparagraph)>  ]
 
 =back
 
-=head1 COMMON PROBLEMS
+=head1 COMMON PROBLEMS AND FAQ
 
 =over 10
 
 =item Citations result in overfull boxes
 
 There is an incompatibility between the C<ulem> package, which C<latexdiff> uses for underlining and striking out in the UNDERLINE style,
-the default style. In order to be able to mark up citations properly, they are placed with an C<\mbox> command in post-processing. As mboxes
-cannot be broken across lines, this procedure frequently results in overfull boxes, possibly obscuring the content as it extends beyond the right margin. If this is a problem, you have two possibilities:
+the default style, and the way citations are generated. In order to be able to mark up citations properly, they are enclosed with an C<\mbox> 
+command. As mboxes cannot be broken across lines, this procedure frequently results in overfull boxes, possibly obscuring the content as it extends beyond the right margin.  The same occurs for some other packages (e.g., siunitx). If this is a problem, you have two possibilities.
 
-1. Use C<COLOR> or C<DVIPSCOL> subtype markup (option C<-s COLOR>): If this markup is chosen, then changed citations are no longer marked up
-with the wavy line (additions) or struck out (deletions), but are still highlighted in the appropriate color.
+1. Use C<CFONT> type markup (option C<-t CFONT>): If this markup is chosen, then changed citations are no longer marked up
+with the wavy line (additions) or struck out (deletions), but are still highlighted in the appropriate color, and deleted text is shown with a different font. Other styles not using the C<ulem> package will also work. 
 
 2. Choose option C<--disable-citation-markup> which turns off the marking up of citations: deleted citations are no longer shown, and
-added ctations are shown without markup. (This was the default behaviour of latexdiff at versions 0.6 and older)
+added citations are shown without markup. (This was the default behaviour of latexdiff at versions 0.6 and older)
+
+For custom packages you can define the commands which need to be protected by C<\mbox> with C<--append-mboxsafecmd> and C<--excludemboxsafecmd> options
+(submit your lists of command as feature request at github page to set the default behaviour of future versions, see section 6)
 
 =item Changes in complicated mathematical equations result in latex processing errors
 
 Try options C<--math-markup=whole>.   If even that fails, you can turn off mark up for equations with C<--math-markup=off>.
 
+=item How can I just show the pages 
+
+Use options -C<-s ZLABEL>  (some postprocessing required) or C<-s ONLYCHANGEDPAGE>. C<latexdiff-vc --ps|--pdf> with C<--only-changes> option takes care of
+the post-processing for you (requires zref packages).
+
 =back
 
 =head1 BUGS
@@ -3528,7 +3735,7 @@ 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 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>
+or send them to I<tilmann -- AT -- 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
 above, and whose differencing still does not result in error-free
@@ -3555,8 +3762,8 @@ I<latexdiff-fast> requires the I<diff> command to be present.
 
 =head1 AUTHOR
 
-Version 1.0.4
-Copyright (C) 2004-2012 Frederik Tilmann
+Version 1.1.0
+Copyright (C) 2004-2015 Frederik Tilmann
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License Version 3
@@ -3780,7 +3987,10 @@ min
 Pr
 sec
 sup
-[Hclbdruvt]
+[Hclbkdruvt]
+[`'^"~=.]
+_
+AMPERSAND
 (SUPER|SUB)SCRIPTNB
 (SUPER|SUB)SCRIPT
 PERCENTAGE
@@ -3821,12 +4031,12 @@ sqrt
 %%END TEXT COMMANDS 
 
 %%BEGIN CONTEXT1 COMMANDS
-% Regex matching commands with a text argument (leave out the \), which will fail out of context, but whose argument should be printed as plain text
+% Regex matching commands with a text argument (leave out the \), which will fail out of context. These commands behave like text commands, except when they occur in a deleted section, where they are disabled, but their argument is shown as deleted text.
 caption
 %%END CONTEXT1 COMMANDS 
 
 %%BEGIN CONTEXT2 COMMANDS
-% Regex matching commands with a text argument (leave out the \), which will fail out of context, but whose argument should be printed as plain text
+% Regex matching commands with a text argument (leave out the \), which will fail out of context.  As corresponding commands for context1.  The only difference is that context2 commands are completely disabled in deleted sections, including their arguments.
 title
 author
 date
@@ -3901,6 +4111,10 @@ institute
 \providecommand{\DIFdel}[1]{}
 %DIF END INVISIBLE PREAMBLE
 
+%DIF BOLD PREAMBLE
+\providecommand{\DIFadd}[1]{{\bf #1}}
+\providecommand{\DIFdel}[1]{}
+%DIF END BOLD PREAMBLE
 
 %% SUBTYPES (Markers for beginning and end of changed blocks)
 
@@ -3938,24 +4152,94 @@ institute
 
 %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)
+% (only works for simple documents with non-repeated page numbers, otherwise use ZLABEL)
 % 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
+%pdftk diff.pdf cat \
+%`perl -lne '\
+% if (m/\\newlabel{DIFchg[b](\d*)}{{.*}{(.*)}}/) { $start{$1}=$2; print $2}\
+% if (m/\\newlabel{DIFchg[e](\d*)}{{.*}{(.*)}}/) { \
+%      if (defined($start{$1})) { \
+%         for ($j=$start{$1}; $j<=$2; $j++) {print "$j";}\
+%      } else { \
+%         print "$2"\
+%      }\
+% }' diff.aux \
+% | uniq \
+% | tr  \\n ' '` \
+% output diff-changedpages.pdf
+% To show only pages with changes (dvips/dvipdf)
+% dvips -pp `\
+% [ put here the perl script from above]
+% | uniq | tr -s \\n ','`
+\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}}
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}}
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}}
+%DIF END LABEL PREAMBLE
+
+%DIF ZLABEL PREAMBLE
+% To show only pages with changes (pdf) (external program pdftk needs to be installed)
+% (uses zref for reference to absolute page numbers)
+% pdflatex diff.tex
+% pdflatex diff.tex
+%pdftk diff.pdf cat \
+%`perl -lne 'if (m/\\zref\@newlabel{DIFchgb(\d*)}{.*\\abspage{(\d*)}}/ ) { $start{$1}=$2; print $2 } \
+%  if (m/\\zref\@newlabel{DIFchge(\d*)}{.*\\abspage{(\d*)}}/) { \
+%      if (defined($start{$1})) { \
+%         for ($j=$start{$1}; $j<=$2; $j++) {print "$j";}\
+%      } else { \
+%         print "$2"\
+%      }\
+% }' diff.aux \
+% | uniq \
+% | tr  \\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}
+\usepackage[user,abspage]{zref}
 \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
+\providecommand{\DIFaddbegin}{\global\advance\DIFcounterb 1\relax\zlabel{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\zlabel{DIFchge\the\DIFcountere}}
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\zlabel{DIFchgb\the\DIFcounterb}}
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\zlabel{DIFchge\the\DIFcountere}}
+%DIF END ZLABEL PREAMBLE
+
+%DIF ONLYCHANGEDPAGE PREAMBLE
+\RequirePackage{atbegshi}
+\RequirePackage{etoolbox}
+\RequirePackage{zref}
+% redefine label command to write immediately to aux file - page references will be lost
+\makeatletter \let\oldlabel\label% Store \label 
+\renewcommand{\label}[1]{% Update \label to write to the .aux immediately 
+\zref@wrapper@immediate{\oldlabel{#1}}} 
+\makeatother 
+\newbool{DIFkeeppage}
+\newbool{DIFchange}
+\boolfalse{DIFkeeppage}
+\boolfalse{DIFchange}
+\AtBeginShipout{%
+  \ifbool{DIFkeeppage}
+        {\global\boolfalse{DIFkeeppage}}  % True DIFkeeppage
+         {\ifbool{DIFchange}{\global\boolfalse{DIFkeeppage}}{\global\boolfalse{DIFkeeppage}\AtBeginShipoutDiscard}} % False DIFkeeppage
+}
+\providecommand{\DIFaddbegin}{\global\booltrue{DIFkeeppage}\global\booltrue{DIFchange}}
+\providecommand{\DIFaddend}{\global\booltrue{DIFkeeppage}\global\boolfalse{DIFchange}}
+\providecommand{\DIFdelbegin}{\global\booltrue{DIFkeeppage}\global\booltrue{DIFchange}}
+\providecommand{\DIFdelend}{\global\booltrue{DIFkeeppage}\global\boolfalse{DIFchange}}
+%DIF END ONLYCHANGEDPAGE PREAMBLE
+
 %% FLOAT TYPES 
 
 %DIF FLOATSAFE PREAMBLE
diff --git a/Master/texmf-dist/scripts/latexdiff/latexrevise.pl b/Master/texmf-dist/scripts/latexdiff/latexrevise.pl
index 85955af25e8..c87ab45e236 100755
--- a/Master/texmf-dist/scripts/latexdiff/latexrevise.pl
+++ b/Master/texmf-dist/scripts/latexdiff/latexrevise.pl
@@ -509,7 +509,7 @@ which should have been removed already.
 
 The current version is a beta version which has not yet been
 extensively tested, but worked fine locally.  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<latexrevise>
+or send them to I<tilmann -- AT -- gfz-potsdam.de>..  Include the serial number of I<latexrevise>
 (Option --version).  If you come across latexdiff
 output which is not processed correctly by I<latexrevise> please include the
 problem file as well as the old and new files on which it is based,