diff -up ./latexdiff.pl.orig ./latexdiff.pl
--- ./latexdiff.pl.orig	2015-12-28 19:15:33.000000000 -0500
+++ ./latexdiff.pl	2016-06-22 15:46:24.444571914 -0400
@@ -1465,7 +1465,7 @@ sub flatten {
   $bblfile=~s/\.tex$//;
   $bblfile.=".bbl";
 
-  if ( ($includeonly) = ($preamble =~ m/\\includeonly{(.*?)}/ ) ) {
+  if ( ($includeonly) = ($preamble =~ m/\\includeonly\{(.*?)}/ ) ) {
     $includeonly =~ s/,/|/g;
   } else {
     $includeonly = '.*?';
@@ -1474,7 +1474,7 @@ sub flatten {
   print STDERR "DEBUG: includeonly $includeonly\n" if $debug;
 
   # recursively replace \\input and \\include files
-  1 while $text=~s/(^(?:[^%\n]|\\%)*)\\input{(.*?)}|\\include{(${includeonly}(?:\.tex)?)}/{ 
+  1 while $text=~s/(^(?:[^%\n]|\\%)*)\\input\{(.*?)}|\\include\{(${includeonly}(?:\.tex)?)}/{ 
 	    $begline=(defined($1)? $1 : "") ;
 	    $fname = $2 if defined($2) ;
 	    $fname = $3 if defined($3) ;
@@ -1491,7 +1491,7 @@ sub flatten {
 	    "$begline$newpage$replacement$newpage";
           }/exgm;
   # replace bibliography with bbl file if it exists
-  $text=~s/(^(?:[^%\n]|\\%)*)\\bibliography{(.*?)}/{ 
+  $text=~s/(^(?:[^%\n]|\\%)*)\\bibliography\{(.*?)}/{ 
            if ( -f $bblfile ){
 	     $replacement=read_file_with_encoding(File::Spec->catfile($bblfile), $encoding);
 	   } else {
@@ -1502,7 +1502,7 @@ sub flatten {
 	   "$begline$replacement";
   }/exgm;
   # replace subfile with contents (subfile package)
-  $text=~s/(^(?:[^%\n]|\\%)*)\\subfile{(.*?)}/{ 
+  $text=~s/(^(?:[^%\n]|\\%)*)\\subfile\{(.*?)}/{ 
            $begline=(defined($1)? $1 : "") ;
      	   $fname = $2; 
            #      # add tex extension unless there is a three letter extension already 
@@ -2244,7 +2244,7 @@ sub take_comments_and_enter_from_frac()
 sub preprocess {
   for (@_) { 
     #    Change \{ to \QLEFTBRACE, \} to \QRIGHTBRACE, and \& to \AMPERSAND
-    s/(?<!\\)\\{/\\QLEFTBRACE /sg;
+    s/(?<!\\)\\\{/\\QLEFTBRACE /sg;
     s/(?<!\\)\\}/\\QRIGHTBRACE /sg;
     s/(?<!\\)\\&/\\AMPERSAND /sg;
 # replace {,} in comments with \\CLEFTBRACE,\\CRIGHTBRACE
@@ -2258,29 +2258,29 @@ sub preprocess {
     s/\\begin\{(verbatim\*?)\}(.*?)\\end\{\1\}/"\\${1}{". tohash(\%verbhash,"${2}") . "}"/esg;
     # Convert _n or _\cmd into \SUBSCRIPTNB{n} or \SUBSCRIPTNB{\cmd} and _{nnn} into \SUBSCRIPT{nn}
     1 while s/(?<!\\)_(\s*([^{\\\s]|\\\w+))/\\SUBSCRIPTNB{$1}/g ;
-    1 while s/(?<!\\)_(\s*{($pat_n)})/\\SUBSCRIPT$1/g ;
+    1 while s/(?<!\\)_(\s*\{($pat_n)})/\\SUBSCRIPT$1/g ;
     # Convert ^n into \SUPERSCRIPTNB{n} and ^{nnn} into \SUPERSCRIPT{nn}
     1 while s/(?<!\\)\^(\s*([^{\\\s]|\\\w+))/\\SUPERSCRIPTNB{$1}/g ;
-    1 while s/(?<!\\)\^(\s*{($pat_n)})/\\SUPERSCRIPT$1/g ;  
+    1 while s/(?<!\\)\^(\s*\{($pat_n)})/\\SUPERSCRIPT$1/g ;  
     # Convert  \sqrt{n} into \SQRT{n}  and  \sqrt nn into SQRTNB{nn}
     1 while s/(?<!\\)\\sqrt(\s*([^{\\\s]|\\\w+))/\\SQRTNB{$1}/g ;
-    1 while s/(?<!\\)\\sqrt(\s*{($pat_n)})/\\SQRT$1/g ;
+    1 while s/(?<!\\)\\sqrt(\s*\{($pat_n)})/\\SQRT$1/g ;
     # Convert $$ $$ into \begin{DOLLARDOLLAR} \end{DOLLARDOLLAR}
     s/\$\$(.*?)\$\$/\\begin{DOLLARDOLLAR}$1\\end{DOLLARDOLLAR}/sg;
     # Convert \[ \] into \begin{SQUAREBRACKET} \end{SQUAREBRACKET}
     s/(?<!\\)\\\[/\\begin{SQUAREBRACKET}/sg;
     s/\\\]/\\end{SQUAREBRACKET}/sg;
     # Convert all picture environmentent (\begin{PICTUREENV} .. \end{PICTUREENV} \PICTUREBLOCKenv
-    s/\\begin{($PICTUREENV)}(.*?)\\end{\1}/\\PICTUREBLOCK$1\{$2\}/sg;
+    s/\\begin\{($PICTUREENV)}(.*?)\\end\{\1}/\\PICTUREBLOCK$1\{$2\}/sg;
     #    For --block-math-markup option -convert all \begin{MATH} .. \end{MATH}
     #    into \MATHBLOCKMATH{...} commands, where MATH is any valid math environment
     #    Also convert all array environments into ARRAYBLOCK environments
     if ( $mathmarkup != FINE ) {
-      s/\\begin{($ARRENV)}(.*?)\\end{\1}/\\ARRAYBLOCK$1\{$2\}/sg;
+      s/\\begin\{($ARRENV)}(.*?)\\end\{\1}/\\ARRAYBLOCK$1\{$2\}/sg;
       
       take_comments_and_enter_from_frac();
       
-      s/\\begin{($MATHENV|$MATHARRENV|SQUAREBRACKET)}(.*?)\\end{\1}/\\MATHBLOCK$1\{$2\}/sg;
+      s/\\begin\{($MATHENV|$MATHARRENV|SQUAREBRACKET)}(.*?)\\end\{\1}/\\MATHBLOCK$1\{$2\}/sg;
     }
     # add final token " STOP"
     $_ .= " STOP"
@@ -2566,15 +2566,15 @@ sub postprocess {
     # environments) are between the \begin{$MATHENV} and \end{MATHMODE} commands. This is necessary as the minimal matching 
     # is not globally minimal but only 'locally' (matching is beginning from the left side of the string)
     if ( $mathmarkup == FINE ) {
-      1 while s/\\begin{((?:$MATHENV)|(?:$MATHARRENV)|SQUAREBRACKET)}((?:.(?!(?:\\end{(?:(?:$MATHENV)|(?:$MATHARRENV)|SQUAREBRACKET)}|\\begin{MATHMODE})))*?)\\end{MATHMODE}/\\begin{$1}$2\\end{$1}/s;
-      1 while s/\\begin{MATHMODE}((?:.(?!\\end{MATHMODE}))*?)\\end{((?:$MATHENV)|(?:$MATHARRENV)|SQUAREBRACKET)}/\\begin{$2}$1\\end{$2}/s;
-      # convert remaining \begin{MATHMODE} \end{MATHMODE} (and not containing & or \\ )into MATHREPL environments
-      s/\\begin{MATHMODE}((?:(.(?!(?<!\\)\&|\\\\))*)?)\\end{MATHMODE}/\\begin{$MATHREPL}$1\\end{$MATHREPL}/sg;
+      1 while s/\\begin\{((?:$MATHENV)|(?:$MATHARRENV)|SQUAREBRACKET)}((?:.(?!(?:\\end\{(?:(?:$MATHENV)|(?:$MATHARRENV)|SQUAREBRACKET)}|\\begin\{MATHMODE})))*?)\\end\{MATHMODE}/\\begin{$1}$2\\end{$1}/s;
+      1 while s/\\begin\{MATHMODE}((?:.(?!\\end\{MATHMODE}))*?)\\end\{((?:$MATHENV)|(?:$MATHARRENV)|SQUAREBRACKET)}/\\begin{$2}$1\\end{$2}/s;
+      # convert remaining \begin\{MATHMODE} \end{MATHMODE} (and not containing & or \\ )into MATHREPL environments
+      s/\\begin\{MATHMODE}((?:(.(?!(?<!\\)\&|\\\\))*)?)\\end\{MATHMODE}/\\begin{$MATHREPL}$1\\end{$MATHREPL}/sg;
       # others into MATHARRREPL
-      s/\\begin{MATHMODE}(.*?)\\end{MATHMODE}/\\begin{$MATHARRREPL}$1\\end{$MATHARRREPL}/sg;
+      s/\\begin\{MATHMODE}(.*?)\\end\{MATHMODE}/\\begin{$MATHARRREPL}$1\\end{$MATHARRREPL}/sg;
 
       # now look for AUXCMD math-mode pairs which have only comments (or empty lines between them), and remove the added commands
-      s/\\begin{((?:$MATHENV)|(?:$MATHARRENV)|SQUAREBRACKET)}$AUXCMD\n((?:\s*%.[^\n]*\n)*)\\end{\1}$AUXCMD\n/$2/sg;       
+      s/\\begin\{((?:$MATHENV)|(?:$MATHARRENV)|SQUAREBRACKET)}$AUXCMD\n((?:\s*%.[^\n]*\n)*)\\end{\1}$AUXCMD\n/$2/sg;       
     } else {
       #   math modes OFF,WHOLE,COARSE: Convert \MATHBLOCKmath{..} commands back to environments
       s/\\MATHBLOCK($MATHENV|$MATHARRENV|SQUAREBRACKET)\{($pat_n)\}/\\begin{$1}$2\\end{$1}/sg;
@@ -2652,19 +2652,19 @@ sub postprocess {
     # undo renaming of the \begin and \end,{,}  and dollars in comments 
     1 while s/(%.*)DOLLARDIF/$1\$/mg ;
 #   Convert \begin{SQUAREBRACKET} \end{SQUAREBRACKET} into \[ \]
-    s/\\end{SQUAREBRACKET}/\\\]/sg;
-    s/\\begin{SQUAREBRACKET}/\\\[/sg;
+    s/\\end\{SQUAREBRACKET}/\\\]/sg;
+    s/\\begin\{SQUAREBRACKET}/\\\[/sg;
 # 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/\\SUPERSCRIPT(\s*{($pat_n)})/^$1/g ;
-    1 while s/\\SUPERSCRIPTNB{(\s*$pat0)}/^$1/g ;
+    1 while s/\\SUPERSCRIPT(\s*\{($pat_n)})/^$1/g ;
+    1 while s/\\SUPERSCRIPTNB\{(\s*$pat0)}/^$1/g ;
     # Convert  \SUBSCRIPNB{n} into _n  and  \SUBCRIPT{nn} into _{nnn}
-    1 while s/\\SUBSCRIPT(\s*{($pat_n)})/_$1/g ;
-    1 while s/\\SUBSCRIPTNB{(\s*$pat0)}/_$1/g ;
+    1 while s/\\SUBSCRIPT(\s*\{($pat_n)})/_$1/g ;
+    1 while s/\\SUBSCRIPTNB\{(\s*$pat0)}/_$1/g ;
     # Convert  \SQRT{n} into \sqrt{n}  and  \SQRTNB{nn} into \sqrt nn
-    1 while s/\\SQRT(\s*{($pat_n)})/\\sqrt$1/g ;
-    1 while s/\\SQRTNB{(\s*$pat0)}/\\sqrt$1/g ;
+    1 while s/\\SQRT(\s*\{($pat_n)})/\\sqrt$1/g ;
+    1 while s/\\SQRTNB\{(\s*$pat0)}/\\sqrt$1/g ;
  
     1 while s/(%.*)\\CRIGHTBRACE (.*)$/$1\}$2/mg ;
     1 while s/(%.*)\\CLEFTBRACE (.*)$/$1\{$2/mg ;
