latexdiff

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

3 files changed, 247 insertions, 109 deletions

diff --git a/Master/texmf-dist/scripts/latexdiff/latexdiff-vc.pl b/Master/texmf-dist/scripts/latexdiff/latexdiff-vc.pl
index 56696daada7..d38fc146441 100755
--- a/Master/texmf-dist/scripts/latexdiff/latexdiff-vc.pl
+++ b/Master/texmf-dist/scripts/latexdiff/latexdiff-vc.pl
@@ -3,9 +3,9 @@
 # latexdiff-vc  - wrapper script for applying latexdiff to rcs managed files
 #                 and for automatised creation of postscript or pdf from difference file
 #
-#   Copyright (C) 2005-13  F J Tilmann (tilmann@gfz-potsdam.de, ftilmann@users.berlios.de)
+#   Copyright (C) 2005-13  F J Tilmann (tilmann@gfz-potsdam.de)
 #
-# Project webpages:   http://latexdiff.berlios.de/
+# Repository:         https://github.com/ftilmann/latexdiff
 # CTAN page:          http://www.ctan.org/tex-archive/support/latexdiff
 #
 #
@@ -25,6 +25,8 @@
 #
 # Detailed usage information at the end of the file
 #
+# version 1.0.4alpha:
+#	- [ 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)
 # version 1.0.2: - option --so to use latexdiff-so
@@ -46,8 +48,8 @@ use strict ;
 use warnings ;
 
 my $versionstring=<<EOF ;
-This is LATEXDIFF-VC 1.0.3
-  (c) 2005-2012 F J Tilmann
+This is LATEXDIFF-VC 1.0.4alpha
+  (c) 2005-2013 F J Tilmann
 EOF
 
 
@@ -55,11 +57,12 @@ EOF
 my ($version,$help,$fast,$so,$postscript,$pdf,$force,$dir,$cvs,$rcs,$svn,$git,$diffcmd,$patchcmd,@revs);
 # Preset Variables
 my $latexdiff="latexdiff"; # Program for making the comparison
+my $latexcmd="latex"; # latex compiler if not further identified
 my $vc="";
 my $tempdir=tempdir(CLEANUP => 1);
 # Variables
 my ($file1,$file2,$diff,$diffbase,$answer,$options,$infile,$append,$dirname,$cwd);
-my (@files,@ldoptions,@tmpfiles,@ptmpfiles,@difffiles); # ,
+my (@files,@ldoptions,@tmpfiles,@ptmpfiles,@difffiles,$extracomp); # ,
 
 Getopt::Long::Configure('pass_through','bundling');
 
@@ -77,6 +80,8 @@ GetOptions('revision|r:s' => \@revs,
            'version' => \$version,
 	   'help|h' => \$help);
 
+$extracomp = join(" ",grep(/BAR/,@ARGV)); # special latexdiff options requiring additional compilation
+
 if ( $help ) {
   pod2usage(1) ;
 }
@@ -137,9 +142,6 @@ if (! $vc && scalar(@revs)>0 ) {
     $vc="SVN";
   } elsif ( $0 =~ /-git$/ ) {
     $vc="GIT";
-  } elsif ( -e "CVSROOT" || defined($ENV{"CVSROOT"}) ) {
-    print STDERR "Guess you are using CVS ...\n";
-    $vc="CVS";
   } elsif ( -e "$file2,v" ) {
     print STDERR "Guess you are using RCS ...\n";
     $vc="RCS";
@@ -149,6 +151,9 @@ if (! $vc && scalar(@revs)>0 ) {
   } elsif ( -d ".git" ) {
     print STDERR "Guess you are using GIT ...\n";
     $vc="GIT";
+  } elsif ( -e "CVSROOT" || defined($ENV{"CVSROOT"}) ) {
+    print STDERR "Guess you are using CVS ...\n";
+    $vc="CVS";
   } else {
     print STDERR "Cannot figure out version control system, so I default to CVS\n";
     $vc="CVS";
@@ -303,31 +308,41 @@ foreach $diff ( @difffiles ) {
   # adapt magically changebar styles to [pdftex] display driver if pdf output was selected
   if ( $pdf ) {
     system("sed \"s/Package\\[dvips\\]/Package[pdftex]/\" \"$diff\" > \"$diff.tmp$$\" ; \\mv \"$diff.tmp$$\" \"$diff\"");
+    $latexcmd = "pdflatex";
+  } elsif ( $postscript ) {
+    $latexcmd = "latex";
   }
+
+  if ( $pdf | $postscript ) {
   print STDERR "PDF: $pdf Postscript: $postscript cwd $cwd\n";
 
   if ( system("grep -q \'^[^%]*\\\\bibliography\' \"$diff\"") == 0 ) { 
-    if ( $postscript) {
-      system("latex --interaction=batchmode \"$diff\"; bibtex \"$diffbase\"");
-      push @ptmpfiles, "$diffbase.bbl","$diffbase.bbl" ; 
-    } elsif ( $pdf ) {
-      system("pdflatex --interaction=batchmode \"$diff\"; bibtex \"$diffbase\"");
-      push @ptmpfiles, "$diffbase.bbl","$diffbase.bbl" ; 
-    }
+    system("$latexcmd --interaction=batchmode \"$diff\"; bibtex \"$diffbase\";");
+    push @ptmpfiles, "$diffbase.bbl","$diffbase.bbl" ; 
+  }
+
+  # if special needs, as CHANGEBAR
+  if ( $extracomp ) {
+    # print "Extracomp\n";
+    system("$latexcmd --interaction=batchmode \"$diff\";");
   }
 
+  # final compilation
+  system("$latexcmd --interaction=batchmode \"$diff\";"); # needed if cross-refs
+  system("$latexcmd \"$diff\";"); # final, with possible error messages
+
   if ( $postscript ) {
     my $dvi="$diffbase.dvi";
     my $ps="$diffbase.ps";
 
-    system("latex --interaction=batchmode \"$diff\"; latex \"$diff\"; dvips -o $ps $dvi");
+    system("dvips -o $ps $dvi");
     push @ptmpfiles, "$diffbase.aux","$diffbase.log",$dvi ;
     print "Generated postscript file $ps\n";
   } 
   elsif ( $pdf ) {
-    system("pdflatex --interaction=batchmode \"$diff\"; pdflatex \"$diff\"");
     push @ptmpfiles, "$diffbase.aux","$diffbase.log";
   }
+  }
   unlink @ptmpfiles;
   chdir $cwd;
 }
@@ -476,9 +491,8 @@ or higher are required.
 
 =head1 BUG REPORTING
 
- Please submit bug reports through
-the latexdiff project page I<http://developer.berlios.de/projects/latexdiff/> or send
-to I<tilmann@gfz-potsdam.de>.  Include the serial number of I<latexdiff-vc>
+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>)
 .
 =head1 AUTHOR
diff --git a/Master/texmf-dist/scripts/latexdiff/latexdiff.pl b/Master/texmf-dist/scripts/latexdiff/latexdiff.pl
index e1f1d9b1b29..6cd69fd9353 100755
--- a/Master/texmf-dist/scripts/latexdiff/latexdiff.pl
+++ b/Master/texmf-dist/scripts/latexdiff/latexdiff.pl
@@ -3,9 +3,9 @@
 # latexdiff - differences two latex files on the word level
 #             and produces a latex file with the differences marked up.
 #
-#   Copyright (C) 2004-12  F J Tilmann (tilmann@gfz-potsdam.de, ftilmann@users.berlios.de)
+#   Copyright (C) 2004-12  F J Tilmann (tilmann@gfz-potsdam.de)
 #
-# Project webpages:   http://latexdiff.berlios.de/
+# Repository/issue tracker:   https://github.com/ftilmann/latexdiff
 # CTAN page:          http://www.ctan.org/tex-archive/support/latexdiff
 #
 #    This program is free software: you can redistribute it and/or modify
@@ -22,14 +22,34 @@
 #
 # Detailed usage information at the end of the file
 #
+# ToDo:
+#
+# Version 1.0.4
+#    - introduce list UNSAFEMATHCMD, which holds list of commands which cannot be marked up with \DIFadd or \DIFdel commands  (only relevant for WHOLE and COARSE math markup modes)
+#    - new subtype LABEL which gives each change a label. This can later be used to only display pages where changes
+#      have been made (instructions for that are put as comments into the diff'ed file) inspired by answer on http://tex.stackexchange.com/questions/166049/invisible-markers-in-pdfs-using-pdflatex
+#    - Configuration variables take into accout some commands from additional packages: 
+#      tikzpicture environment now treated as PICTUREENV, and \smallmatrix in ARRENV (amsmath)
+#    - --flatten: support for \subfile command (subfiles package)  (in response to http://tex.stackexchange.com/questions/167620/latexdiff-with-subfiles )
+#    - --flatten: \bibliography commands expand if corresponding bbl file present
+#    - angled bracket optional commands now parsed correctly (patch #3570) submitted by Dave Kleinschmidt (thanks)
+#    - \RequirePackage now treated as synonym of \usepackage with respect to setting packages
+#    - special rules for apacite package (redefine citation commands)
+#    - recognise /dev/null as 'file-like' arguments for --preamble and --config options
+#    - fix units package incompatibility with ulem for text maths statements $ ..$ (thanks to Stuart Prescott for reporting this)
+#    - amsmath environment cases treated correctly (Bug fix #19029) (thanks to Jalar)
+#    - {,} in comments no longer confuse latexdiff (Bug fix #19146)
+#    - \% in one-letter sub/Superscripts was not converted correctly
+#
 # Version 1.0.3
 #    - fix bug in add_safe_commands that made latexdiff hang on DeclareMathOperator 
 #      command in preamble
-#    - \(..\) inline math expressions were not parsed correctly, if the contained a linebreak
+#    - \(..\) inline math expressions were not parsed correctly, if they contained a linebreak
 #    - applied patch contributed by tomflannaghan via Berlios: [ Patch #3431 ] Adds correct handling of \left< and \right>
 #    - \$ is treated correctly as a literal dollar sign (thanks to Reed Cartwright and Joshua Miller for reporting this bug 
-#       and sketching out the solution)
-#    - \^ and \_ are correctly interpreted as accent and underlined space, respectively, not as superscript of subscript (thanks to Wail Yahyaoui for pointing out this bug)
+#      and sketching out the solution)
+#    - \^ and \_ are correctly interpreted as accent and underlined space, respectively, not as superscript of subscript
+#      (thanks to Wail Yahyaoui for pointing out this bug)
 #
 # Version 1.0.1 - treat \big,\bigg etc. equivalently to \left and
 #              \right - include starred version in MATHENV - apply
@@ -549,28 +569,30 @@ my ($algodiffversion)=split(/ /,$Algorithm::Diff::VERSION);
 
 
 my ($versionstring)=<<EOF ;
-This is LATEXDIFF 1.0.3  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
-  (c) 2004-2013 F J Tilmann
+This is LATEXDIFF 1.0.4  (Algorithm::Diff $Algorithm::Diff::VERSION, Perl $^V)
+  (c) 2004-2014 F J Tilmann
 EOF
 
 # Configuration variables: these have to be visible from the subroutines
 my $MINWORDSBLOCK=3; # minimum number of tokens to form an independent block
                      # shorter identical blocks will be merged to the previous word
 my $FLOATENV='(?:figure|table|plate)[\w\d*@]*' ;   # Environments in which FL variants of defined commands are used
-my $PICTUREENV='(?:picture|DIFnomarkup)[\w\d*@]*' ;   # Environments in which all change markup is removed
+my $PICTUREENV='(?:picture|tikzpicture|DIFnomarkup)[\w\d*@]*' ;   # Environments in which all change markup is removed
 my $MATHENV='(?:equation[*]?|displaymath|DOLLARDOLLAR)[*]?' ;           # Environments turning on display math mode (code also knows about \[ and \])
 my $MATHREPL='displaymath';  # Environment introducing deleted maths blocks
 my $MATHARRENV='(?:eqnarray|align|alignat|gather|multline|flalign)[*]?' ;           # Environments turning on eqnarray math mode
 my $MATHARRREPL='eqnarray*';  # Environment introducing deleted maths blocks
-my $ARRENV='(?:array|[pbvBV]matrix)'; # Environments making arrays in math mode.  The underlining style does not cope well with those - as a result in-text math environments are surrounded by \mbox{ } if any of these commands is used in an inline math block
+my $ARRENV='(?:array|[pbvBV]?matrix|smallmatrix|cases|split)'; # Environments making arrays in math mode.  The underlining style does not cope well with those - as a result in-text math environments are surrounded by \mbox{ } if any of these commands is used in an inline math block
 my $COUNTERCMD='(?:footnote|part|chapter|section|subsection|subsubsection|paragraph|subparagraph)';  # textcmds which are associated with a counter
                                         # If any of these commands occur in a deleted block
                                         # they will be succeeded by an \addtocounter{...}{-1}
                                         # for the associated counter such that the overall numbers
                                         # should be the same as in the new file
+my @UNSAFEMATHCMD=('qedhere');           # Commands which are definitely unsafe for marking up (amsmath qedhere only tested to not work with UNDERLINE markup)
 my $CITECMD=0 ;  # \cite-type commands which need to be protected within an mbox in UNDERLINE and other modes using ulem; pattern simply designed to never match; will be overwritten later for selected styles
 my $CITE2CMD=0;  # \cite-type commands which should be reinstated in deleted blocks
-
+my $MBOXINLINEMATH=0; # if set to 1 then surround marked-up inline maths expression with \mbox ( to get around compatibility
+                      # problems between some maths packages and ulem package
 
 
 # Markup strings
@@ -633,7 +655,7 @@ my ($type,$subtype,$floattype,$config,$preamblefile,$encoding,$nolabel,$visiblel
     $replacecontext1,$appendcontext1,
     $replacecontext2,$appendcontext2,
     $help,$verbose,$driver,$version,$ignorewarnings,
-    $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug);  ###$disablemathmark,
+    $enablecitmark,$disablecitmark,$allowspaces,$flatten,$debug,$earlylatexdiffpreamble);  ###$disablemathmark,
 # MNEMNONICS for mathmarkup
 my $mathmarkup;
 use constant {
@@ -662,6 +684,11 @@ $mathmarkup=COARSE;
 $verbose=0;
 # output debug and intermediate files, set to 0 in final distribution
 $debug=0; 
+# insert preamble directly after documentclass - experimental feature, set to 0 in final distribution
+# Note that this failed with mini example (or other files, where packages used in latexdiff preamble
+# are called again with incompatible options in preamble of resulting file)
+$earlylatexdiffpreamble=0;
+
 # define character properties
 sub IsNonAsciiPunct { return <<'END'    # Unicode punctuation but excluding ASCII punctuation
 +utf8::IsPunct
@@ -769,29 +796,6 @@ foreach $excludesafe ( @excludesafelist ) {
   init_regex_arr_ext(\@SAFECMDEXCL, $excludesafe);
 }
 
-# Special: treat all cite commands as safe except in UNDERLINE and FONTSTRIKE mode
-# (there is a conflict between citation and ulem package, see
-# package documentation)
-# Use post-processing
-
-if ( uc($type) ne "UNDERLINE" && uc($type) ne "FONTSTRIKE" && uc($type) ne "CULINECHBAR" ) {
-  push (@SAFECMDLIST, qr/^cite.*$/);
-} else {
-  ### Experimental: disable text and emph commands
-  push (@SAFECMDLIST, qr/^cite.*$/) unless $disablecitmark;
-  push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
-  # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
-  if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
-    # remove \cite command again from list of safe commands
-    pop @SAFECMDLIST;
-    # deleted cite commands
-    $CITE2CMD='(?:cite\w*|nocite)' unless $disablecitmark ; # \cite-type commands which should be reinstated in deleted blocks
-  } else {
-    $CITECMD='(?:cite\w*|nocite)' unless $disablecitmark ; # \cite commands which need to be protected within an mbox in UNDERLINE and other modes using ulem
-  }
-}
-$CITECMD='(?:cite\w*|nocite)' if $enablecitmark ; # as above for explicit selection
-
 # setting up @TEXTCMDLIST and @TEXTCMDEXCL
 if (defined($replacetext)) {
   init_regex_arr_ext(\@TEXTCMDLIST,$replacetext);
@@ -830,7 +834,7 @@ foreach $appendcontext2 ( @appendcontext2list ) {
 # setting configuration variables
 @config=();
 foreach $config ( @configlist ) {
-  if (-f $config ) {
+  if (-f $config || lc $config eq '/dev/null' ) {
     open(FILE,$config) or die ("Couldn't open configuration file $config: $!");
     while (<FILE>) {
       chomp;
@@ -941,6 +945,7 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $pat5 = '(?:[^{}]|\{'.$pat4.'\})*';
   my $pat6 = '(?:[^{}]|\{'.$pat5.'\})*';
   my $brat0 = '(?:[^\[\]]|\\\[|\\\])*'; 
+  my $abrat0 = '(?:[^<>])*';
 
   my $quotemarks = '(?:\'\')|(?:\`\`)';
   my $punct='[0.,\/\'\`:;\"\?\(\)\[\]!~\p{IsNonAsciiPunct}\p{IsNonAsciiS}]';
@@ -952,7 +957,7 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $word='(?:[-\w\d*]|\\\\[\"\'\`~^][A-Za-z\*])+';
   my $cmdleftright='\\\\(?:left|right|[Bb]igg?[lrm]?|middle)\s*(?:[<>()\[\]|]|\\\\(?:[|{}]|\w+))';
 
-  my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
+  my $cmdoptseq='\\\\[\w\d\*]+'.$extraspace.'(?:(?:<'.$abrat0.'>|\['.$brat0.'\]|\{'. $pat6 . '\}|\(' . $coords .'\))'.$extraspace.')*';
   my $backslashnl='\\\\\n';
   my $oneletcmd='\\\\.\*?(?:\['.$brat0.'\]|\{'. $pat6 . '\})*';
   my $math='\$(?:[^$]|\\\$)*?\$|\\\\[(](?:.|\n)*?\\\\[)]';
@@ -961,8 +966,6 @@ push(@SAFECMDLIST, qr/^QLEFTBRACE$/, qr/^QRIGHTBRACE$/);
   my $comment='%.*?\n';
   my $pat=qr/(?:\A\s*)?(?:${and}|${quotemarks}|${number}|${word}|$cmdleftright|${cmdoptseq}|${math}|${backslashnl}|${oneletcmd}|${comment}|${punct}|${mathpunct}|\{|\})\s*/ ;
 
-
-
 # now we are done setting up and can start working   
 my ($oldfile, $newfile) = @ARGV;
 # check for existence of input files
@@ -1016,6 +1019,9 @@ if ($flatten) {
   $newbody=flatten($newbody,$newpreamble,$newfile,$encoding);
 }
 
+
+
+
 my @auxlines;
 if ( length $oldpreamble && length $newpreamble ) {
   # pre-process preamble by looking for commands used in \maketitle (title, author, date etc commands) 
@@ -1029,13 +1035,25 @@ if ( length $oldpreamble && length $newpreamble ) {
   # Base this assessment on the new preamble
   add_safe_commands($newpreamble);
 
+  # get a list of packages from preamble if not predefine
   %packages=list_packages(@newpreamble) unless %packages;
+  ###  if ( %packages ) {print STDERR "DEBUG Packages: ",%packages,"\n" ;}
   if (defined $packages{"hyperref"} ) {
+    # deleted lines should not generate or appear in link names:
     print STDERR "hyperref package detected.\n" if $verbose ;
     $latexdiffpreamble =~ s/\{\\DIFadd\}/{\\DIFaddtex}/g;
     $latexdiffpreamble =~ s/\{\\DIFdel\}/{\\DIFdeltex}/g;
     $latexdiffpreamble .= join "\n",(extrapream("HYPERREF"),"");
   }
+
+  if (defined $packages{"units"}  && ( $latexdiffpreamble =~ /\\RequirePackage(?:\[$brat0\])?\{ulem\}/ ) ) {
+    # protect inlined maths environments by surrounding with an \mbox
+    # this is done to get around an incompatibility between the ulem and units package
+    # where spaces in the argument to underlined or crossed-out \unit commands cause an error message
+    print STDERR "units package detected at the same time as style using ulem.\n" if $verbose ;
+    $MBOXINLINEMATH=1;
+  }
+
   print STDERR "Differencing preamble.\n" if $verbose;
 
   # insert dummy first line such that line count begins with line 1 (rather than perl's line 0) - just so that line numbers inserted by linediff are correct
@@ -1053,7 +1071,14 @@ if ( length $oldpreamble && length $newpreamble ) {
     push @diffpreamble,"%DIF DELETED TITLE COMMANDS FOR MARKUP";
     push @diffpreamble,join("\n",@auxlines);
   }
-  push @diffpreamble,$latexdiffpreamble;
+  if ( $earlylatexdiffpreamble) {
+    # insert latexdiff command directly after documentclass at beginning of preamble
+    # note that grep is only run for its side effect
+    ( grep { s/^([^%]*\\documentclass.*)$/$1$latexdiffpreamble/ } @diffpreamble )==1 or die "Could not find documentclass statement in preamble";
+  } else {
+    # insert latexdiff commands at the end of preamble (default behaviour)
+    push @diffpreamble,$latexdiffpreamble;
+  }
   push @diffpreamble,'\begin{document}';
 }
 elsif ( !length $oldpreamble && !length $newpreamble ) {
@@ -1063,6 +1088,43 @@ elsif ( !length $oldpreamble && !length $newpreamble ) {
   exit(2);
 }
 
+# Special: treat all cite commands as safe except in UNDERLINE and FONTSTRIKE mode
+# (there is a conflict between citation and ulem package, see
+# package documentation)
+# Use post-processing
+# and $packages{"apacite"}!~/natbibpapa/
+my ($citpat,$citpatsafe);
+
+if ( defined $packages{"apacite"}  ) {
+  print STDERR "DEBUG apacite citation commands\n"  if $debug;
+  $citpatsafe=qr/^(?:mask)?(?:full|short)?cite(?:A|author|year)?(?:NP)?$/;
+  $citpat='(?:mask)?(?:full|short|no)?cite(?:A|author|year|meta)?(?:NP)?';
+} else {
+  # citation command pattern for all other citation schemes
+  $citpatsafe=qr/^cite.*$/;
+  $citpat='(?:cite\w*|nocite)';
+};
+
+if ( uc($type) ne "UNDERLINE" && uc($type) ne "FONTSTRIKE" && uc($type) ne "CULINECHBAR" ) {
+  push (@SAFECMDLIST, $citpatsafe);
+} else {
+  ### Experimental: disable text and emph commands
+  push (@SAFECMDLIST, $citpatsafe) unless $disablecitmark;
+  push(@SAFECMDEXCL, qr/^emph$/, qr/^text..$/);
+  # replace \cite{..} by \mbox{\cite{..}} in added or deleted blocks in post-processing
+  if ( uc($subtype) eq "COLOR" or uc($subtype) eq "DVIPSCOL" ) {
+    # remove \cite command again from list of safe commands
+    pop @SAFECMDLIST;
+    # deleted cite commands
+    $CITE2CMD=$citpat unless $disablecitmark ; # \cite-type commands which should be reinstated in deleted blocks
+  } else {
+    $CITECMD=$citpat unless $disablecitmark ; # \cite commands which need to be protected within an mbox in UNDERLINE and other modes using ulem
+  }
+}
+$CITECMD=$citpat if $enablecitmark ; # as above for explicit selection
+
+print STDERR "CITECMD:|$CITECMD|\n" if $debug;
+
 if (defined $packages{"amsmath"}  or defined $packages{"amsart"} or defined $packages{"amsbook"} ) {
   print STDERR "amsmath package detected.\n" if $verbose ;
   $MATHARRREPL='align*';
@@ -1154,7 +1216,7 @@ sub read_file_with_encoding {
 }
 
 # %packages=list_packages(@preamble)
-# scans the arguments for \documentclass and \usepackage statements and constructs a hash
+# scans the arguments for \documentclass,\RequirePackage and \usepackage statements and constructs a hash
 # whose keys are the included packages, and whose values are the associated optional arguments
 sub list_packages {
   my (@preamble)=@_;
@@ -1162,7 +1224,7 @@ sub list_packages {
   foreach $line ( @preamble ) {
     # get rid of comments
     $line=~s/(?<!\\)%.*$// ;
-    if ( $line =~ m/\\(?:documentclass|usepackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
+    if ( $line =~ m/\\(?:documentclass|usepackage|RequirePackage)(?:\[(.+?)\])?\{(.*?)\}/ ) {
 #      print STDERR "Found something: |$line|\n";
       if (defined($1)) {
 	$packages{$2}=$1;
@@ -1199,7 +1261,7 @@ sub add_safe_commands {
       }
     }
 
-    while ( $preamble =~ m/\\(?:|re|provide)newcommand\s*{\\(\w*)\}(?:|\[\d*\])\s*\{(${pat6})\}/osg ) {
+    while ( $preamble =~ m/\\(?:new|renew|provide)command\s*{\\(\w*)\}(?:|\[\d*\])\s*\{(${pat6})\}/osg ) {
       my $maybe_to_test  = $1;
       my $should_be_safe = $2;
       my $success = 0;
@@ -1229,14 +1291,20 @@ sub add_safe_commands {
 
 # flatten($text,$preamble,$filename,$encoding)
 # expands \input and \include commands within text
+# expands \bibliography command with corresponding bbl file if available
+# expands \subfile command (from subfiles package - not part of standard text distribution)
 # preamble is scanned for includeonly commands
 # encoding is the encoding
 sub flatten {
   my ($text,$preamble,$filename,$encoding)=@_;
-  my ($includeonly,$dirname,$fname,$newpage,$replacement,$begline);
+  my ($includeonly,$dirname,$fname,$newpage,$replacement,$begline,$bblfile,$subfile);
+  my ($subpreamble,$subbody,$subpost);
   require File::Basename ; 
   require File::Spec ; 
   $dirname = File::Basename::dirname($filename);
+  $bblfile = $filename;
+  $bblfile=~s/\.tex$//;
+  $bblfile.=".bbl";
 
   if ( ($includeonly) = ($preamble =~ m/\\includeonly{(.*?)}/ ) ) {
     $includeonly =~ s/,/|/g;
@@ -1246,9 +1314,10 @@ sub flatten {
 
   print STDERR "DEBUG: includeonly $includeonly\n" if $debug;
 
+  # recursively replace \\input and \\include files
   $text=~s/(^(?:[^%\n]|\\%)*)\\input{(.*?)}|\\include{(${includeonly}(?:\.tex)?)}/{ 
 	    $fname = $2 if defined($2) ;
-	    $fname = $3 if defined($3) ;       
+	    $fname = $3 if defined($3) ;
             #      # add tex extension unless there is a three letter extension already 
             $fname .= ".tex" unless $fname =~ m|\.\w{3}|;
             print STDERR "DEBUG Beg of line match |$1|\n" if defined($1) && $debug ;
@@ -1262,6 +1331,34 @@ sub flatten {
 	    $newpage=(defined($3)? " \\newpage " : "") ;
 	    "$begline$newpage$replacement$newpage";
           }/exgm;
+  # replace bibliography with bbl file if it exists
+  $text=~s/(^(?:[^%\n]|\\%)*)\\bibliography{(.*?)}/{ 
+           if ( -f $bblfile ){
+	     $replacement=read_file_with_encoding(File::Spec->catfile($bblfile), $encoding);
+	   } else {
+	     warn "Bibliography file $bblfile cannot be found. No flattening of \\bibliography done. Run bibtex on old and new files first";
+	     $replacement="\\bibliography{$2}";
+	   }
+	   $begline=(defined($1)? $1 : "") ;
+	   "$begline$replacement";
+  }/exgm;
+  # replace subfile with contents (subfile package)
+  $text=~s/(^(?:[^%\n]|\\%)*)\\subfile{(.*?)}/{ 
+	   $fname = $2; 
+           #      # add tex extension unless there is a three letter extension already 
+           $fname .= ".tex" unless $fname =~ m|\.\w{3}|;
+           print STDERR "DEBUG Beg of line match |$1|\n" if defined($1) && $debug ;
+           print STDERR "Include file as subfile $fname\n" if $verbose;
+           print STDERR "DEBUG looking for file ",File::Spec->catfile($dirname,$fname), "\n" if $debug;
+           # content of file becomes replacement value (use recursion)
+           # now strip away everything outside and including \begin{document} and \end{document} pair#
+	   #             # note: no checking for comments is made
+           $subfile=read_file_with_encoding(File::Spec->catfile($dirname,$fname), $encoding) or die "Couldn't find file ",File::Spec->catfile($dirname,$fname),": $!";
+           ($subpreamble,$subbody,$subpost)=splitdoc($subfile,'\\\\begin\{document\}','\\\\end\{document\}');
+	   $replacement=flatten($subbody, $preamble,$filename,$encoding);
+           $begline=(defined($1)? $1 : "") ;
+	   "$begline$replacement";
+  }/exgm;
 
   return($text);
 }
@@ -1287,7 +1384,7 @@ sub extrapream {
   while (@_) {
     $copy=0;
     $type=shift ;
-    if ( -f $type ) {
+    if ( -f $type || lc $type eq '/dev/null' ) {
       open (FILE,$type) or die "Cannot open preamble file $type: $!";
       print STDERR "Reading preamble file $type\n" if $verbose ;
       while (<FILE>) {
@@ -1855,7 +1952,7 @@ sub marktags {
 	  # Keep these commands even in deleted blocks, hence set $opencmd and $closecmd (5th and 6th argument of marktags) to 
 	  # ""
 	  local @SAFECMDLIST=(".*"); 
-	  local @SAFECMDEXCL=('\\','\\\\');
+	  local @SAFECMDEXCL=('\\','\\\\',@UNSAFEMATHCMD);
 	  push(@$retval,$command,marktags("","",$open,$close,"","",$comment,\@argtext)#@argtext
                        ,$closingbracket);
         } else {
@@ -1890,9 +1987,8 @@ sub marktags {
 # preprocess($string, ..)
 # carry out the following pre-processing steps for all arguments:
 # 1. Remove leading white-space
-#    Change \{ to \LEFTBRACE and \} to \RIGHTBRACE
-# #. change begin and end commands  within comments to BEGINDIF, ENDDIF
-#    so they don't disturb the pattern matching (if there are several \begin or \end in one line
+#    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
+# #.   Change {,} in comments to \CLEFTBRACE, \CRIGHTBRACE
 # 2. mark all first empty line (in block of several) with \PAR tokens
 # 3. Convert all '\%' into '\PERCENTAGE ' and all '\$' into \DOLLAR to make parsing regular expressions easier
 # 4. Convert all \verb|some verbatim text| commands (where | can be an arbitrary character)
@@ -1919,11 +2015,9 @@ sub preprocess {
     #    Change \{ to \QLEFTBRACE and \} to \QRIGHTBRACE
     s/(?<!\\)\\{/\\QLEFTBRACE /sg;
     s/(?<!\\)\\}/\\QRIGHTBRACE /sg;
-    # change begin and end commands  within comments such that they
-    # don't disturb the pattern matching (if there are several \begin or \end in one line
-    # this substitution is insufficient but that appears unlikely)
-    s/(%.*)\\begin\{(.*)$/$1\\BEGINDIF\{$2/mg ;
-    s/(%.*)\\end\{(.*)$/$1\\ENDDIF\{$2/mg ;
+# replace {,} in comments with \\CLEFTBRACE,\\CRIGHTBRACE
+    1 while s/((?<!\\)%.*)\{(.*)$/$1\\CLEFTBRACE $2/mg ;
+    1 while s/((?<!\\)%.*)\}(.*)$/$1\\CRIGHTBRACE $2/mg ;
 
     s/\n(\s*?)\n((?:\s*\n)*)/\n$1\\PAR\n$2/g ;
     s/(?<!\\)\\%/\\PERCENTAGE /g ;  # (?<! is negative lookbehind assertion to prevent \\% from being converted
@@ -2036,7 +2130,7 @@ sub fromhash {
 # 9.. remove all \PAR tokens
 # 10.  package specific processing:  endfloat: make sure \begin{figure} and \end{figure} are always
 #      on a line by themselves, similarly for table environment
-#  4, undo renaming of the \begin and \end in comments
+#  4, undo renaming of the \begin, \end,{,}  in comments
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
 #
 # Note have to manually synchronize substitution commands below and 
@@ -2162,8 +2256,14 @@ sub postprocess {
       }
       # or protect \cite commands with \mbox
       if ($CITECMD) {
-	$delblock=~s/(\\($CITECMD)${extraspace}(?:\[$brat0\]${extraspace}){0,2}\{$pat6\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	$delblock=~s/(\\($CITECMD)${extraspace}(?:<$abrat0>${extraspace})?(?:\[$brat0\]${extraspace}){0,2}\{$pat6\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
       } 
+      # if MBOXINLINEMATH is set, protect inlined math environments with an extra mbox
+      if ( $MBOXINLINEMATH ) {
+	# note additional \newline after command is omitted from output if right at the end of deleted block (otherwise a spurious empty line is generated)
+	$delblock=~s/($math)(?:[\s\n]*)?/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
+      }
+
 #     splice in modified delblock
       substr($_,$begin,$len)=$delblock;
       pos = $begin + length($delblock);
@@ -2185,7 +2285,16 @@ sub postprocess {
       }
       if ($CITECMD) {
 	my $addblockbefore=$addblock;
-	$addblock=~ s/(\\($CITECMD)${extraspace}(?:\[$brat0\]${extraspace}){0,2}\{$pat2\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	#(?:mask)?(?:full|short|no)?cite(?:A|author|year|meta)(?:NP)?$/
+	###my $CITECMD; $CITECMD="cite(?:A)$";
+	$addblock=~ s/(\\($CITECMD)${extraspace}(?:<$abrat0>${extraspace})?(?:\[$brat0\]${extraspace}){0,2}\{$pat2\})(\s*)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/msg ;
+	print STDERR "DEBUG: CITECMD $CITECMD\nDEBUG: addblock before:|$addblockbefore|\n" if $debug;
+	print STDERR "DEBUG: addblock after: |$addblock|\n" if $debug;
+      }
+      # if MBOXINLINEMATH is set, protect inlined math environments with an extra mbox
+      if ( $MBOXINLINEMATH ) {
+	##$addblock=~s/($math)/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
+	$addblock=~s/($math)(?:[\s\n]*)?/\\mbox{$AUXCMD\n$1\n}$AUXCMD\n/sg;
       }
 #     splice in modified addblock
       substr($_,$begin,$len)=$addblock;
@@ -2193,13 +2302,6 @@ sub postprocess {
     }
 
 
-    ### old place for BEGINDIF, ENDDIF replacement
-    # change begin and end commands  within comments such that they
-    # don't disturb the pattern matching (if there are several \begin or \end in one line
-    # this substitution is insufficient but that appears unlikely)
-    # This needs to be repeated here to also get rid of DIFdelcmd-protected environments
-    s/(%.*)\\begin\{(.*)$/$1\\BEGINDIF\{$2/mg ;
-    s/(%.*)\\end\{(.*)$/$1\\ENDDIF\{$2/mg ;
 
     # Replace MATHMODE environments from step 1a above by the correct Math environment
 
@@ -2266,8 +2368,8 @@ sub postprocess {
     s/(\\verb\*?)\{([-\d]*?)\}/"${1}". fromhash(\%verbhash,$2)/esg;
     s/${DELCMDOPEN}\\(verbatim\*?)\{([-\d]*?)\}/"${DELCMDOPEN}\\begin{${1}}".fromhash(\%verbhash,$2,$DELCMDOPEN)."${DELCMDOPEN}\\end{${1}}"/esg;
     s/\\(verbatim\*?)\{([-\d]*?)\}/"\\begin{${1}}".fromhash(\%verbhash,$2)."\\end{${1}}"/esg;
-    # Convert '\PERCENTAGE ' back into '\%'			       
-    s/\\PERCENTAGE /\\%/g;
+    # Convert '\PERCENTAGE ' back into '\%' (the final question mark catches a special situation where due to a latter pre-processing step the ' ' becomes separated	       
+    s/\\PERCENTAGE ?/\\%/g;
     # Convert '\DOLLAR ' back into '\$'			       
     s/\\DOLLAR /\\\$/g;
     # remove all \PAR tokens (taking care to properly keep commented out PAR's
@@ -2290,9 +2392,7 @@ sub postprocess {
       # split lines with remaining characters after float enviroment conmmand
       s/(\\(?:begin|end)\{(?:figure|table)\})(.+)$/$1\n$2/mg;
     }
-    # undo renaming of the \begin and \end  and dollars in comments 
-    s/(%.*)\\BEGINDIF\{(.*)$/$1\\begin\{$2/mg ;
-    s/(%.*)\\ENDDIF\{(.*)$/$1\\end\{$2/mg ;
+    # undo renaming of the \begin and \end,{,}  and dollars in comments 
     1 while s/(%.*)DOLLARDIF/$1\$/mg ;
     # undo renaming of the \cite.. commands in comments 
     if ( $CITECMD ) {
@@ -2304,11 +2404,15 @@ sub postprocess {
 # 4. Convert \begin{DOLLARDOLLAR} \end{DOLLARDOLLAR} into $$ $$
     s/\\begin\{DOLLARDOLLAR\}(.*?)\\end\{DOLLARDOLLAR\}/\$\$$1\$\$/sg;
 # 5. Convert  \SUPERSCRIPTNB{n} into ^n  and  \SUPERSCRIPT{nn} into ^{nnn}
-    1 while s/\\SUPERSCRIPTNB{($pat0)}/^$1/g ;
     1 while s/\\SUPERSCRIPT{($pat6)}/^{$1}/g ;
+    1 while s/\\SUPERSCRIPTNB{($pat0)}/^$1/g ;
     # Convert  \SUBSCRIPNB{n} into _n  and  \SUBCRIPT{nn} into _{nnn}
-    1 while s/\\SUBSCRIPTNB{($pat0)}/_$1/g ;
     1 while s/\\SUBSCRIPT{($pat6)}/_{$1}/g ;
+    1 while s/\\SUBSCRIPTNB{($pat0)}/_$1/g ;
+    1 while s/(%.*)\\CRIGHTBRACE (.*)$/$1\}$2/mg ;
+    1 while s/(%.*)\\CLEFTBRACE (.*)$/$1\{$2/mg ;
+
+
 #    Change \QLEFTBRACE, \QRIGHTBRACE to \{,\}
     s/\\QLEFTBRACE /\\{/sg;
     s/\\QRIGHTBRACE /\\}/sg;
@@ -2571,7 +2675,7 @@ format as new.tex but has all changes relative to old.tex marked up or commented
 --subtype=markstyle
 -s markstyle           Add code to preamble for selected style for bracketing
                        commands (e.g. to mark changes in  margin)
-                       Available styles: SAFE MARGINAL DVIPSCOL COLOR
+                       Available styles: SAFE MARGINAL DVIPSCOL COLOR LABEL
                        [ Default: SAFE ]
 
 --floattype=markstyle
@@ -2670,7 +2774,7 @@ format as new.tex but has all changes relative to old.tex marked up or commented
                        Use of the --packages option disables automatic scanning, so if for any
                        reason package specific parsing needs to be switched off, use --packages=none.
                        The following packages trigger special behaviour:
-                       endfloat hyperref amsmath
+                       endfloat hyperref amsmath apacite
                        [ Default: scan the preamble for \\usepackage commands to determine
                          loaded packages.]
 
@@ -2726,7 +2830,7 @@ Miscelleneous options
 
 --no-label             Suppress inclusion of old and new file names as comment in output file
 
---visble-label         Include old and new filenames (or labels set with --label option) as 
+--visible-label         Include old and new filenames (or labels set with --label option) as 
                        visible output
 
 --flatten              Replace \\input and \\include commands within body by the content
@@ -2751,7 +2855,6 @@ Miscelleneous options
 
 --version              Show version number.
 
-For further information, consult   http://latexdiff.berlios.de
 EOF
 }
 
@@ -2914,7 +3017,7 @@ B<-s markstyle>
 Add code to preamble for selected style for bracketing
 commands (e.g. to mark changes in  margin). This option defines
 C<\DIFaddbegin>, C<\DIFaddend>, C<\DIFdelbegin> and C<\DIFdelend> commands.
-Available styles: C<SAFE MARGINAL COLOR DVIPSCOL>
+Available styles: C<SAFE MARGINAL COLOR DVIPSCOL LABEL>
 
 [ Default: C<SAFE> ]
 
@@ -2983,6 +3086,10 @@ define new C<\DIFadd> and C<\DIFdel> commands, which provide a wrapper for these
 using them for the text but not for the link defining command (where any markup would cause
 errors).
 
+=item C<apacite>
+
+Redefine the commands recognised as citation commands.
+
 =back
 
 [ Default: scan the preamble for C<\\usepackage> commands to determine
@@ -3155,6 +3262,7 @@ Protect citation commands in changed sections with \\mbox command [i.e. use defa
 =head2 Miscellaneous
 
 =over 4
+
 =item B<--verbose> or B<-V>
 
 Output various status information to stderr during processing.
@@ -3419,9 +3527,7 @@ Option allow-spaces not implemented entirely consistently. It breaks
 the rules that number and type of white space does not matter, as
 different numbers of inter-argument spaces are treated as significant.
 
-Please submit bug reports on the latexdiff project page I<http://latexdiff.berlios.de>, 
-send them to user discussion list C<latexdiff-users@lists.berlios,de> (prior subscription 
-to list required, also on project webpage)
+Please submit bug reports using the issue tracker of the github repository page I<https://github.com/ftilmann/latexdiff.git>, 
 or send them to I<tilmann@gfz-potsdam.de>.  Include the serial number of I<latexdiff>
 (from comments at the top of the source or use B<--version>).  If you come across latex
 files that are error-free and conform to the specifications set out
@@ -3449,7 +3555,7 @@ I<latexdiff-fast> requires the I<diff> command to be present.
 
 =head1 AUTHOR
 
-Version 1.0.2
+Version 1.0.4
 Copyright (C) 2004-2012 Frederik Tilmann
 
 This program is free software; you can redistribute it and/or modify
@@ -3457,7 +3563,7 @@ it under the terms of the GNU General Public License Version 3
 
 Contributors of fixes and additions: V. Kuhlmann, J. Paisley, N. Becker, T. Doerges, K. Huebner, 
 T. Connors, Sebastian Gouezel and many others.
-Thanks to the many people who send in bug reports, feature suggestions, and other feedback.
+Thanks to the many people who sent in bug reports, feature suggestions, and other feedback.
 
 =cut
 
@@ -3830,7 +3936,26 @@ institute
 \providecommand{\DIFdelend}{\protect\color{black}}
 %DIF END COLOR PREAMBLE
 
-
+%DIF LABEL PREAMBLE
+% To show only pages with changes (pdf) (external program pdftk needs to be installed)
+% (only works for simple documents with non-repeated page numbers)
+% pdflatex diff.tex
+% pdflatex diff.tex
+% pdftk diff.pdf cat `perl -lne 'if (m/\\newlabel{DIFchg[be]\d*}{{.*}{(.*)}}/) { print $1 }' diff.aux | uniq | tr -s \\n ' '` output diff-changedpages.pdf
+% To show only pages with changes (dvips/dvipdf)
+% latex diff.tex
+% latex diff.tex
+% dvips -pp `perl -lne 'if (m/\\newlabel{DIFchg[be]\d*}{{.*}{(.*)}}/) { print $1 }' diff.aux | uniq | tr -s \\n ','` diff.dvi 
+\typeout{Check comments in preamble of output for instructions how to show only pages where changes have been made}
+\newcount\DIFcounterb
+\global\DIFcounterb 0\relax
+\newcount\DIFcountere
+\global\DIFcountere 0\relax
+\providecommand{\DIFaddbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}} %DIF PREAMBLE
+\providecommand{\DIFaddend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}} %DIF PREAMBLE
+\providecommand{\DIFdelbegin}{\global\advance\DIFcounterb 1\relax\label{DIFchgb\the\DIFcounterb}} %DIF PREAMBLE
+\providecommand{\DIFdelend}{\global\advance\DIFcountere 1\relax\label{DIFchge\the\DIFcountere}} %DIF PREAMBLE
+%DIF END LABEL PREAMBLE
 %% FLOAT TYPES 
 
 %DIF FLOATSAFE PREAMBLE
@@ -3860,7 +3985,7 @@ institute
 \providecommand{\DIFaddendFL}{}
 \providecommand{\DIFdelbeginFL}{}
 \providecommand{\DIFdelendFL}{}
-%DIF END FLOATSAFE PREAMBLE
+%DIF END TRADITIONALSAFE PREAMBLE
 
 %% SPECIAL PACKAGE PREAMBLE COMMANDS
 
diff --git a/Master/texmf-dist/scripts/latexdiff/latexrevise.pl b/Master/texmf-dist/scripts/latexdiff/latexrevise.pl
index 0f333fbb994..85955af25e8 100755
--- a/Master/texmf-dist/scripts/latexdiff/latexrevise.pl
+++ b/Master/texmf-dist/scripts/latexdiff/latexrevise.pl
@@ -2,9 +2,9 @@
 #   latexrevise - takes output file of latexdiff and removes either discarded
 #                 or appended passages, then deletes all other latexdiff markup
 #
-#   Copyright (C) 2004  F J Tilmann (tilmann@gfz-potsdam.de, ftilmann@users.berlios.de)
+#   Copyright (C) 2004  F J Tilmann (tilmann@gfz-potsdam.de)
 #
-# Project webpages:   http://latexdiff.berlios.de/
+# Repository:         https://github.com/ftilmann/latexdiff
 # CTAN page:          http://www.ctan.org/tex-archive/support/latexdiff
 #
 #    This program is free software: you can redistribute it and/or modify
@@ -508,10 +508,9 @@ which should have been removed already.
 =head1 BUGS
 
 The current version is a beta version which has not yet been
-extensively tested, but worked fine locally.  Please submit bug reports through
-the latexdiff project page I<http://developer.berlios.de/projects/latexdiff/> or send
-to I<tilmann@gfz-potsdam.de>.  Include the serial number of I<latexrevise>
-(from comments at the top of the source).  If you come across latexdiff
+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>
+(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,
 ideally edited to only contain the offending passage as long as that still