latexindent (23feb17)

git-svn-id: svn://tug.org/texlive/trunk@43326 c570f23f-e606-0410-a88d-b1316a301751

1 files changed, 27 insertions, 2105 deletions

diff --git a/Build/source/texk/texlive/linked_scripts/latexindent/latexindent.pl b/Build/source/texk/texlive/linked_scripts/latexindent/latexindent.pl
index cdd979a8ccf..06adc58a1b8 100755
--- a/Build/source/texk/texlive/linked_scripts/latexindent/latexindent.pl
+++ b/Build/source/texk/texlive/linked_scripts/latexindent/latexindent.pl
@@ -11,57 +11,34 @@
 #
 #	See http://www.gnu.org/licenses/.
 #
-#	For details of how to use this file, please see readme.txt
+#	Chris Hughes, 2017
+#
+#	For all communication, please visit: https://github.com/cmhughes/latexindent.pl
 
-# load packages/modules: assume strict and warnings are part of every perl distribution
 use strict;
 use warnings;
+use FindBin;                   # help find defaultSettings.yaml
+use Getopt::Long;              # to get the switches/options/flags
 
-# list of modules
-my @listOfModules = ('FindBin','YAML::Tiny','File::Copy','File::Basename','Getopt::Long','File::HomeDir');
-
-# check the other modules are available
-foreach my $moduleName (@listOfModules) {
-    # references:
-    #       http://stackoverflow.com/questions/251694/how-can-i-check-if-i-have-a-perl-module-before-using-it
-    #       http://stackoverflow.com/questions/1917261/how-can-i-dynamically-include-perl-modules-without-using-eval
-    eval {
-        (my $file = $moduleName) =~ s|::|/|g;
-        require $file . '.pm';
-        $moduleName->import();
-        1;
-    } or die "$moduleName Perl Module not currently installed; please install the module, and then try running latexindent.pl again; exiting";
-}
-
-# now that we have confirmed the modules are available, load them
-use FindBin;        # help find defaultSettings.yaml
-use YAML::Tiny;     # interpret defaultSettings.yaml and other potential settings files
-use File::Copy;     # to copy the original file to backup (if overwrite option set)
-use File::Basename; # to get the filename and directory path
-use Getopt::Long;   # to get the switches/options/flags
-use File::HomeDir;  # to get users home directory, regardless of OS
+# use lib to make sure that @INC contains the latexindent directory
+use lib $FindBin::RealBin;
+use LatexIndent::Document;
 
 # get the options
-my $overwrite;
-my $outputToFile;
-my $silentMode;
-my $tracingMode;
-my $tracingModeVeryDetailed;
-my $readLocalSettings=0;
-my $onlyDefault;
-my $showhelp;
-my $cruftDirectory;
+my %switches = (readLocalSettings=>0);
 
 GetOptions (
- "overwrite|w"=>\$overwrite,
-"outputfile|o"=>\$outputToFile,
-"silent|s"=>\$silentMode,
-"trace|t"=>\$tracingMode,
-"ttrace|tt"=>\$tracingModeVeryDetailed,
-"local|l:s"=>\$readLocalSettings,
-"onlydefault|d"=>\$onlyDefault,
-"help|h"=>\$showhelp,
-"cruft|c=s"=>\$cruftDirectory,
+    "silent|s"=>\$switches{silentMode},
+    "trace|t"=>\$switches{trace},
+    "ttrace|tt"=>\$switches{ttrace},
+    "local|l:s"=>\$switches{readLocalSettings},
+    "onlydefault|d"=>\$switches{onlyDefault},
+    "overwrite|w"=>\$switches{overwrite},
+    "outputfile|o=s"=>\$switches{outputToFile},
+    "modifylinebreaks|m"=>\$switches{modifyLineBreaks},
+    "logfile|g=s"=>\$switches{logFileName},
+    "help|h"=>\$switches{showhelp},
+    "cruft|c=s"=>\$switches{cruftDirectory},
 );
 
 # check local settings doesn't interfer with reading the file;
@@ -74,20 +51,9 @@ GetOptions (
 #
 # In such circumstances, we correct the mistake by assuming that 
 # the only argument is the file to be indented, and place it in @ARGV
-if($readLocalSettings and scalar(@ARGV) < 1) {
-    push(@ARGV,$readLocalSettings);
-    $readLocalSettings = '';
-}
-
-# this can also happen if the script is called as
-#
-#       latexindent.pl -o -l myfile.tex outputfile.tex
-#
-# in which case, the GetOptions routine mistakes myfile.tex
-# as the optional parameter to the l flag.
-if($readLocalSettings and scalar(@ARGV) < 2 and $outputToFile) {
-    unshift(@ARGV,$readLocalSettings);
-    $readLocalSettings = '';
+if($switches{readLocalSettings} and scalar(@ARGV) < 1) {
+    push(@ARGV,$switches{readLocalSettings});
+    $switches{readLocalSettings} = '';
 }
 
 # default value of readLocalSettings
@@ -95,2054 +61,10 @@ if($readLocalSettings and scalar(@ARGV) < 2 and $outputToFile) {
 #       latexindent -l myfile.tex
 #
 # means that we wish to use localSettings.yaml
-if(defined($readLocalSettings) and ($readLocalSettings eq '')){
-    $readLocalSettings = 'localSettings.yaml';
-}
-
-# detailed tracing mode also implies regular tracing mode
-$tracingMode = $tracingModeVeryDetailed ? 1 : $tracingMode;
-
-# version number
-my $versionNumber = "2.2";
-
-# Check the number of input arguments- if it is 0 then simply
-# display the list of options (like a manual)
-if(scalar(@ARGV) < 1 or $showhelp) {
-    print <<ENDQUOTE
-latexindent.pl version $versionNumber
-usage: latexindent.pl [options] [file][.tex]
-      -h, --help
-          help (see the documentation for detailed instructions and examples)
-      -o, --outputfile
-          output to another file; sample usage
-                latexindent.pl -o myfile.tex outputfile.tex
-      -w, --overwrite
-          overwrite the current file- a backup will be made, but still be careful
-      -s, --silent
-          silent mode- no output will be given to the terminal
-      -t, --trace
-          tracing mode- verbose information given to the log file
-      -l, --local[=myyaml.yaml]
-          use localSettings.yaml (assuming it exists in the directory of your file);
-          alternatively, use myyaml.yaml, if it exists
-      -d, --onlydefault
-          ONLY use defaultSettings.yaml, ignore ALL user files
-      -c, --cruft=<cruft directory> 
-          used to specify the location of backup files and indent.log
-ENDQUOTE
-    ;
-    exit(2);
-}
-
-# set up default for cruftDirectory using the one from the input file,
-# unless it has been specified using -c="/some/directory"
-$cruftDirectory=dirname $ARGV[0] unless(defined($cruftDirectory));
-
-die "Could not find directory $cruftDirectory\nExiting, no indentation done." if(!(-d $cruftDirectory));
-
-# we'll be outputting to the logfile and to standard output
-my $logfile;
-my $out = *STDOUT;
-
-# open the log file
-open($logfile,">","$cruftDirectory/indent.log") or die "Can't open indent.log";
-
-# output time to log file
-my $time = localtime();
-print $logfile $time;
-
-# output version to log file
-print $logfile <<ENDQUOTE
-
-$FindBin::Script version $versionNumber, a script to indent .tex files
-$FindBin::Script lives here: $FindBin::RealBin/
-
-ENDQUOTE
-;
-
-# latexindent.exe is a standalone executable, and caches 
-# the required perl modules onto the users system; they will
-# only be displayed if the user specifies the trace option
-if($FindBin::Script eq 'latexindent.exe' and !$tracingMode ) {
-print $logfile <<ENDQUOTE
-$FindBin::Script is a standalone script and caches the required perl modules
-onto your system. If you'd like to see their location in your log file, indent.log, 
-call the script with the tracing option, e.g latexindent.exe -t myfile.tex
-
-ENDQUOTE
-;
-}
-
-# output location of modules
-if($FindBin::Script eq 'latexindent.pl' or ($FindBin::Script eq 'latexindent.exe' and $tracingMode )) {
-    print $logfile "Modules are being loaded from the following directories:\n ";
-    foreach my $moduleName (@listOfModules) {
-            (my $file = $moduleName) =~ s|::|/|g;
-            require $file . '.pm';
-            print $logfile "\t",$INC{$file .'.pm'},"\n";
-          }
-}
-
-# a quick options check
-if($outputToFile and $overwrite) {
-    print $logfile <<ENDQUOTE
-
-WARNING:
-\t You have called latexindent.pl with both -o and -w
-\t -o (output to file) will take priority, and -w (over write) will be ignored
-
-ENDQUOTE
-;
-    $overwrite = 0;
-}
-
-# can't call the script with MORE THAN 2 files
-if(scalar(@ARGV)>2) {
-    for my $fh ($out,$logfile) {print $fh <<ENDQUOTE
-
-ERROR:
-\t You're calling latexindent.pl with more than two file names
-\t The script can take at MOST two file names, but you
-\t need to call it with the -o switch; for example
-
-\t latexindent.pl -o originalfile.tex outputfile.tex
-
-No indentation done :(
-Exiting...
-ENDQUOTE
-    };
-    exit(2);
-}
-
-# don't call the script with 2 files unless the -o flag is active
-if(!$outputToFile and scalar(@ARGV)==2)
-{
-for my $fh ($out,$logfile) {
-print $fh <<ENDQUOTE
-
-ERROR:
-\t You're calling latexindent.pl with two file names, but not the -o flag.
-\t Did you mean to use the -o flag ?
-
-No indentation done :(
-Exiting...
-ENDQUOTE
-};
-    exit(2);
-}
-
-# if the script is called with the -o switch, then check that
-# a second file is present in the call, e.g
-#           latexindent.pl -o myfile.tex output.tex
-if($outputToFile and scalar(@ARGV)==1) {
-    for my $fh ($out,$logfile) {print $fh <<ENDQUOTE
-ERROR: When using the -o flag you need to call latexindent.pl with 2 arguments
-
-latexindent.pl -o "$ARGV[0]" [needs another name here]
-
-No indentation done :(
-Exiting...
-ENDQUOTE
-};
-    exit(2);
+if(defined($switches{readLocalSettings}) and ($switches{readLocalSettings} eq '')){
+    $switches{readLocalSettings} = 'localSettings.yaml';
 }
 
-# yaml work
-print $logfile "YAML files:\n";
-
-# Read in defaultSettings.YAML file
-my $defaultSettings = YAML::Tiny->new;
-
-# Open defaultSettings.yaml
-$defaultSettings = YAML::Tiny->read( "$FindBin::RealBin/defaultSettings.yaml" );
-print $logfile "\tReading defaultSettings.yaml from $FindBin::RealBin/defaultSettings.yaml\n\n" if($defaultSettings);
-
-# if latexindent.exe is invoked from TeXLive, then defaultSettings.yaml won't be in 
-# the same directory as it; we need to navigate to it
-if(!$defaultSettings) {
-    $defaultSettings = YAML::Tiny->read( "$FindBin::RealBin/../../texmf-dist/scripts/latexindent/defaultSettings.yaml");
-    print $logfile "\tReading defaultSettings.yaml (2nd attempt, TeXLive, Windows) from $FindBin::RealBin/../../texmf-dist/scripts/latexindent/defaultSettings.yaml\n\n" if($defaultSettings);
-}
-
-# if both of the above attempts have failed, we need to exit
-if(!$defaultSettings) {
-  for my $fh ($out,$logfile) {
- print $fh <<ENDQUOTE
- ERROR  There seems to be a yaml formatting error in defaultSettings.yaml
-        Please check it for mistakes- you can find a working version at https://github.com/cmhughes/latexindent.pl
-        if you would like to overwrite your current version
-
-        Exiting, no indendation done.
-ENDQUOTE
-};
- exit(2);
-}
-
-# the MASTER settings will initially be from defaultSettings.yaml
-# and we update them with USER settings (if any) below
-my %masterSettings = %{$defaultSettings->[0]};
-
-# empty array to store the paths
-my @absPaths;
-
-# scalar to read user settings
-my $userSettings;
-
-# get information about user settings- first check if indentconfig.yaml exists
-my $indentconfig = File::HomeDir->my_home . "/indentconfig.yaml";
-# if indentconfig.yaml doesn't exist, check for the hidden file, .indentconfig.yaml
-$indentconfig = File::HomeDir->my_home . "/.indentconfig.yaml" if(! -e $indentconfig);
-
-if ( -e $indentconfig and !$onlyDefault ) {
-      print $logfile "\tReading path information from $indentconfig\n";
-      # if both indentconfig.yaml and .indentconfig.yaml exist
-      if ( -e File::HomeDir->my_home . "/indentconfig.yaml" and  -e File::HomeDir->my_home . "/.indentconfig.yaml") {
-            print $logfile File::HomeDir->my_home,"/.indentconfig.yaml has been found, but $indentconfig takes priority\n";
-      } elsif ( -e File::HomeDir->my_home . "/indentconfig.yaml" ) {
-            print $logfile "\tAlternatively, ",File::HomeDir->my_home,"/.indentconfig.yaml can be used\n";
-
-      } elsif ( -e File::HomeDir->my_home . "/.indentconfig.yaml" ) {
-            print $logfile "\tAlternatively, ",File::HomeDir->my_home,"/indentconfig.yaml can be used\n";
-      }
-
-      # read the absolute paths from indentconfig.yaml
-      $userSettings = YAML::Tiny->read( "$indentconfig" );
-
-      # integrity check
-      if($userSettings) {
-        print $logfile "\t",Dump \%{$userSettings->[0]};
-        print $logfile "\n";
-        @absPaths = @{$userSettings->[0]->{paths}};
-      } else {
-        print $logfile <<ENDQUOTE
-WARNING:  $indentconfig
-          contains some invalid .yaml formatting- unable to read from it.
-          No user settings loaded.
-ENDQUOTE
-;
-      }
-} else {
-      if($onlyDefault) {
-        print $logfile "\tOnly default settings requested, not reading USER settings from $indentconfig\n";
-        print $logfile "\tIgnoring $readLocalSettings\n" if($readLocalSettings);
-        $readLocalSettings = 0;
-      } else {
-        # give the user instructions on where to put indentconfig.yaml or .indentconfig.yaml
-        print $logfile "\tHome directory is ",File::HomeDir->my_home,"\n";
-        print $logfile "\tTo specify user settings you would put indentconfig.yaml here: \n\t",File::HomeDir->my_home,"/indentconfig.yaml\n\n";
-        print $logfile "\tAlternatively, you can use the hidden file .indentconfig.yaml as: \n\t",File::HomeDir->my_home,"/.indentconfig.yaml\n\n";
-      }
-}
-
-# get information about LOCAL settings, assuming that $readLocalSettings exists
-my $directoryName = dirname $ARGV[0];
-
-# add local settings to the paths, if appropriate
-if ( (-e "$directoryName/$readLocalSettings") and $readLocalSettings and !(-z "$directoryName/$readLocalSettings")) {
-    print $logfile "\tAdding $directoryName/$readLocalSettings to paths\n\n";
-    push(@absPaths,"$directoryName/$readLocalSettings");
-} elsif ( !(-e "$directoryName/$readLocalSettings") and $readLocalSettings) {
-      print $logfile "\tWARNING yaml file not found: \n\t$directoryName/$readLocalSettings not found\n";
-      print $logfile "\t\tcarrying on without it.\n";
-}
-
-# read in the settings from each file
-foreach my $settings (@absPaths) {
-  # check that the settings file exists and that it isn't empty
-  if (-e $settings and !(-z $settings)) {
-      print $logfile "\tReading USER settings from $settings\n";
-      $userSettings = YAML::Tiny->read( "$settings" );
-
-      # if we can read userSettings
-      if($userSettings) {
-            # update the MASTER setttings to include updates from the userSettings
-            while(my($userKey, $userValue) = each %{$userSettings->[0]}) {
-                    # the update approach is slightly different for hashes vs scalars/arrays
-                    if (ref($userValue) eq "HASH") {
-                        while(my ($userKeyFromHash,$userValueFromHash) = each %{$userSettings->[0]{$userKey}}) {
-                          $masterSettings{$userKey}{$userKeyFromHash} = $userValueFromHash;
-                        }
-                    } else {
-                          $masterSettings{$userKey} = $userValue;
-                    }
-            }
-            # output settings to $logfile
-            if($masterSettings{logFilePreferences}{showEveryYamlRead}){
-                print $logfile Dump \%{$userSettings->[0]};
-                print $logfile "\n";
-            } else {
-                print $logfile "\t\tNot showing settings in the log file, see showEveryYamlRead.\n";
-            }
-       } else {
-             # otherwise print a warning that we can not read userSettings.yaml
-             print $logfile "WARNING\n\t$settings \n\t contains invalid yaml format- not reading from it\n";
-       }
-  } else {
-      # otherwise keep going, but put a warning in the log file
-      print $logfile "\nWARNING\n\t",File::HomeDir->my_home,"/indentconfig.yaml\n";
-      if (-z $settings) {
-          print $logfile "\tspecifies $settings \n\tbut this file is EMPTY- not reading from it\n\n"
-      } else {
-          print $logfile "\tspecifies $settings \n\tbut this file does not exist- unable to read settings from this file\n\n"
-      }
-  }
-}
-
-# some people may wish to see showAlmagamatedSettings
-# which details the overall state of the settings modified
-# from the default in various user files
-if($masterSettings{logFilePreferences}{showAlmagamatedSettings}){
-    print $logfile "Almagamated/overall settings to be used:\n";
-    print $logfile Dump \%masterSettings ;
-}
-
-# scalar variables
-my $defaultIndent = $masterSettings{defaultIndent};
-my $alwaysLookforSplitBraces = $masterSettings{alwaysLookforSplitBraces};
-my $alwaysLookforSplitBrackets = $masterSettings{alwaysLookforSplitBrackets};
-my $backupExtension = $masterSettings{backupExtension};
-my $indentPreamble = $masterSettings{indentPreamble};
-my $onlyOneBackUp = $masterSettings{onlyOneBackUp};
-my $maxNumberOfBackUps = $masterSettings{maxNumberOfBackUps};
-my $removeTrailingWhitespace = $masterSettings{removeTrailingWhitespace};
-my $cycleThroughBackUps = $masterSettings{cycleThroughBackUps};
-
-# hash variables
-my %lookForAlignDelims= %{$masterSettings{lookForAlignDelims}};
-my %indentRules= %{$masterSettings{indentRules}};
-my %verbatimEnvironments= %{$masterSettings{verbatimEnvironments}};
-my %noIndentBlock= %{$masterSettings{noIndentBlock}};
-my %checkunmatched= %{$masterSettings{checkunmatched}};
-my %checkunmatchedELSE= %{$masterSettings{checkunmatchedELSE}};
-my %checkunmatchedbracket= %{$masterSettings{checkunmatchedbracket}};
-my %noAdditionalIndent= %{$masterSettings{noAdditionalIndent}};
-my %indentAfterHeadings= %{$masterSettings{indentAfterHeadings}};
-my %indentAfterItems= %{$masterSettings{indentAfterItems}};
-my %itemNames= %{$masterSettings{itemNames}};
-my %constructIfElseFi= %{$masterSettings{constructIfElseFi}};
-my %fileExtensionPreference= %{$masterSettings{fileExtensionPreference}};
-my %fileContentsEnvironments= %{$masterSettings{fileContentsEnvironments}};
-
-# original name of file
-my $fileName = $ARGV[0];
-
-# sort the file extensions by preference 
-my @fileExtensions = sort { $fileExtensionPreference{$a} <=> $fileExtensionPreference{$b} } keys(%fileExtensionPreference);
-
-# get the base file name, allowing for different extensions (possibly no extension)
-my ($dir, $name, $ext) = fileparse($fileName, @fileExtensions);
-
-# quick check to make sure given file type is supported
-if( -e $ARGV[0] and !$ext ){
-for my $fh ($out,$logfile) {print $fh <<ENDQUOTE
-The file $ARGV[0] exists , but the extension does not correspond to any given in fileExtensionPreference;
-consinder updating fileExtensionPreference.
-
-Exiting, no indentation done.
-ENDQUOTE
-};
-exit(2);
-}
-
-# if no extension, search according to fileExtensionPreference
-if (!$ext) {
-    print $logfile "File extension work:\n";
-    print $logfile "\tlatexindent called to act upon $fileName with an, as yet, unrecognised file extension;\n";
-    print $logfile "\tsearching for file with an extension in the following order (see fileExtensionPreference):\n\t\t";
-    print $logfile join("\n\t\t",@fileExtensions),"\n";
-    my $fileFound = 0;
-    # loop through the known file extensions (see @fileExtensions)
-    foreach my $fileExt (@fileExtensions ){
-        if ( -e $fileName.$fileExt ) {
-           print $logfile "\t",$fileName,$fileExt," found!\n";
-           $fileName .= $fileExt;
-           print $logfile "\tUpdated $ARGV[0] to ",$fileName,"\n";
-           $fileFound = 1;
-           last;
-        }
-    }
-    unless($fileFound){
-      print $logfile "\tI couldn't find a match for $ARGV[0] in fileExtensionPreference (see defaultSettings.yaml)\n";
-      foreach my $fileExt (@fileExtensions ){
-        print $logfile "\t\tI searched for $ARGV[0]$fileExt\n";
-      }
-      print $logfile "\tbut couldn't find any of them.\n";
-      print $logfile "\tConsider updating fileExtensionPreference. \nError: Exiting, no indendation done.";
-      die "I couldn't find a match for $ARGV[0] in fileExtensionPreference.\nExiting, no indendation done.\n" 
-    }
-  } else {
-    # if the file has a recognised extension, check that the file exists
-    unless( -e $ARGV[0] ){
-      print $logfile "Error: I couldn't find $ARGV[0], are you sure it exists?. No indentation done. \nExiting.\n";
-      die "Error: I couldn't find $ARGV[0], are you sure it exists?. Exiting.\n" ;
-    }
-  }
-
-# if we want to over write the current file create a backup first
-if ($overwrite) {
-    print $logfile "\nBackup procedure:\n";
-    # cruft directory
-    print $logfile "\tDirectory for backup files and indent.log: $cruftDirectory\n\n";
-
-    my $backupFile; 
-
-    # backup file name is the base name
-    $backupFile = basename($fileName,@fileExtensions);
-
-    # add the user's backup directory to the backup path
-    $backupFile = "$cruftDirectory/$backupFile";
-
-    # if both ($onlyOneBackUp and $maxNumberOfBackUps) then we have
-    # a conflict- er on the side of caution and turn off onlyOneBackUp
-    if($onlyOneBackUp and $maxNumberOfBackUps>1) {
-        print $logfile "\t WARNING: onlyOneBackUp=$onlyOneBackUp and maxNumberOfBackUps: $maxNumberOfBackUps\n";
-        print $logfile "\t\t setting onlyOneBackUp=0 which will allow you to reach $maxNumberOfBackUps back ups\n";
-        $onlyOneBackUp = 0;
-    }
-
-    # if the user has specified that $maxNumberOfBackUps = 1 then
-    # they only want one backup
-    if($maxNumberOfBackUps==1) {
-        $onlyOneBackUp=1 ;
-        print $logfile "\t FYI: you set maxNumberOfBackUps=1, so I'm setting onlyOneBackUp: 1 \n";
-    } elsif($maxNumberOfBackUps<=0 and !$onlyOneBackUp) {
-        $onlyOneBackUp=0 ;
-        $maxNumberOfBackUps=-1;
-    }
-
-    # if onlyOneBackUp is set, then the backup file will
-    # be overwritten each time
-    if($onlyOneBackUp) {
-        $backupFile .= $backupExtension;
-        print $logfile "\tcopying $fileName to $backupFile\n";
-        print $logfile "\t$backupFile was overwritten\n\n" if (-e $backupFile);
-    } else {
-        # start with a backup file .bak0 (or whatever $backupExtension is present)
-        my $backupCounter = 0;
-        $backupFile .= $backupExtension.$backupCounter;
-
-        # if it exists, then keep going: .bak0, .bak1, ...
-        while (-e $backupFile or $maxNumberOfBackUps>1) {
-            if($backupCounter==$maxNumberOfBackUps) {
-                print $logfile "\t maxNumberOfBackUps reached ($maxNumberOfBackUps)\n";
-
-                # some users may wish to cycle through back up files, e.g:
-                #    copy myfile.bak1 to myfile.bak0
-                #    copy myfile.bak2 to myfile.bak1
-                #    copy myfile.bak3 to myfile.bak2
-                #
-                #    current back up is stored in myfile.bak4
-                if($cycleThroughBackUps) {
-                    print $logfile "\t cycleThroughBackUps detected (see cycleThroughBackUps) \n";
-                    for(my $i=1;$i<=$maxNumberOfBackUps;$i++) {
-                        # remove number from backUpFile
-                        my $oldBackupFile = $backupFile;
-                        $oldBackupFile =~ s/$backupExtension.*/$backupExtension/;
-                        my $newBackupFile = $oldBackupFile;
-
-                        # add numbers back on
-                        $oldBackupFile .= $i;
-                        $newBackupFile .= $i-1;
-
-                        # check that the oldBackupFile exists
-                        if(-e $oldBackupFile){
-                        print $logfile "\t\t copying $oldBackupFile to $newBackupFile \n";
-                            copy($oldBackupFile,$newBackupFile) or die "Could not write to backup file $backupFile. Please check permissions. Exiting.\n";
-                        }
-                    }
-                }
-
-                # rest maxNumberOfBackUps
-                $maxNumberOfBackUps=1 ;
-                last; # break out of the loop
-            } elsif(!(-e $backupFile)) {
-                $maxNumberOfBackUps=1 ;
-                last; # break out of the loop
-            }
-            print $logfile "\t $backupFile already exists, incrementing by 1...\n";
-            $backupCounter++;
-            $backupFile =~ s/$backupExtension.*/$backupExtension$backupCounter/;
-        }
-        print $logfile "\n\t copying $fileName to $backupFile\n\n";
-    }
-
-    # output these lines to the log file
-    print $logfile "\tBackup file: ",$backupFile,"\n";
-    print $logfile "\tOverwriting file: ",$fileName,"\n\n";
-    copy($fileName,$backupFile) or die "Could not write to backup file $backupFile. Please check permissions. Exiting.\n";
-}
-
-if(!($outputToFile or $overwrite)) {
-    print $logfile "Just out put to the terminal :)\n\n" if !$silentMode  ;
-}
-
-
-# scalar variables
-my $line;                   # $line: takes the $line of the file
-my $inpreamble=!$indentPreamble;
-                            # $inpreamble: switch to determine if in
-                            #               preamble or not
-my $inverbatim=0;           # $inverbatim: switch to determine if in
-                            #               a verbatim environment or not
-my $delimiters=0;           # $delimiters: switch that governs if
-                            #              we need to check for & or not
-my $trailingcomments;       # $trailingcomments stores the comments at the end of
-                            #           a line
-my $lineCounter=0;          # $lineCounter keeps track of the line number
-my $inIndentBlock=0;        # $inindentblock: switch to determine if in
-                            #               a inindentblock or not
-my $inFileContents=0;       # $inFileContents: switch to determine if we're in a filecontents environment
-
-# array variables
-my @lines;                  # @lines: stores the newly indented lines
-my @mainfile;               # @mainfile: stores input file; used to
-                            #            grep for \documentclass
-
-# array of hashes, containing details of commands & environments
-my @masterIndentationArrayOfHashes;
-
-# check to see if the current file has \documentclass, if so, then
-# it's the main file, if not, then it doesn't have preamble
-open(MAINFILE, $fileName) or die "Could not open input file, $fileName";
-    @mainfile=<MAINFILE>;
-close(MAINFILE);
-
-# if the MAINFILE doesn't have a \documentclass statement, then
-# it shouldn't have preamble
-if(scalar(@{[grep(m/^\s*\\documentclass/, @mainfile)]})==0) {
-    $inpreamble=0;
-
-    print $logfile "Trace:\tNo documentclass detected, assuming no preamble\n" if($tracingMode);
-} else {
-    print $logfile "Trace:\t documentclass detected, assuming preamble\n" if($tracingMode);
-}
-
-# the previous OPEN command puts us at the END of the file
-open(MAINFILE, $fileName) or die "Could not open input file, $fileName";
-
-# loop through the lines in the INPUT file
-while(<MAINFILE>) {
-    # increment the line counter
-    $lineCounter++;
-
-    # very detailed output to logfile
-    if($tracingModeVeryDetailed){
-        if( @masterIndentationArrayOfHashes){
-            print $logfile "\nLine $lineCounter\t (detailed trace) indentation hash: \n" if($tracingMode);
-            for my $href ( @masterIndentationArrayOfHashes) {
-                   print $logfile Dump \%{$href};
-            }
-        }
-    }
-
-    # tracing mode
-    print $logfile $masterSettings{logFilePreferences}{traceModeBetweenLines} if($tracingMode and !($inpreamble or $inverbatim or $inIndentBlock));
-
-    # check to see if we're still in the preamble
-    # or in a verbatim environment or in IndentBlock
-    if(!($inpreamble or $inverbatim or $inIndentBlock)) {
-        # if not, remove all leading spaces and tabs
-        # from the current line, assuming it isn't empty
-        s/^\t*// if($_ !~ /^((\s*)|(\t*))*$/);
-        s/^\s*// if($_ !~ /^((\s*)|(\t*))*$/);
-
-        # tracing mode
-        print $logfile "Line $lineCounter\t removing leading spaces\n" if($tracingMode);
-    } else {
-        # otherwise check to see if we've reached the main
-        # part of the document
-        if(m/^\s*\\begin\{document\}/ and !$inFileContents and !$inverbatim) {
-            $inpreamble = 0;
-
-            # tracing mode
-            print $logfile "Line $lineCounter\t \\begin{document} found, switching indentation searches on. \n" if($tracingMode);
-        } else {
-            # tracing mode
-            if($inpreamble) {
-                print $logfile "Line $lineCounter\t still in PREAMBLE, leaving exisiting leading space (see indentPreamble)\n" if($tracingMode);
-            } elsif($inverbatim) {
-                print $logfile "Line $lineCounter\t in VERBATIM-LIKE environment, leaving exisiting leading space\n" if($tracingMode);
-            } elsif($inIndentBlock) {
-                print $logfile "Line $lineCounter\t in NO INDENT BLOCK, leaving exisiting leading space\n" if($tracingMode);
-            }
-        }
-    }
-
-    # \END{ENVIRONMENTS}, or CLOSING } or CLOSING ]
-    # \END{ENVIRONMENTS}, or CLOSING } or CLOSING ]
-    # \END{ENVIRONMENTS}, or CLOSING } or CLOSING ]
-
-    # check to see if we're ending a filecontents environment
-    if( $_ =~ m/^\s*\\end\{(.*?)\}/ and  $fileContentsEnvironments{$1} and $inFileContents){
-        print $logfile "Line $lineCounter\t Found END of filecontents environment (see fileContentsEnvironments)\n" if($tracingMode);
-        $inFileContents = 0;
-    }
-
-    # set the delimiters switch
-    $delimiters = @masterIndentationArrayOfHashes?$masterIndentationArrayOfHashes[-1]{alignmentDelimiters}:0;
-
-    if($inverbatim){
-        print $logfile "Line $lineCounter\t $masterSettings{logFilePreferences}{traceModeDecreaseIndent} PHASE 1: in VERBATIM-LIKE environment, looking for $masterIndentationArrayOfHashes[-1]{end} \n" if($tracingMode);
-    } elsif($inIndentBlock) {
-        print $logfile "Line $lineCounter\t in NO INDENT BLOCK, doing nothing\n" if($tracingMode);
-    } elsif($delimiters) {
-        print $logfile "Line $lineCounter\t $masterSettings{logFilePreferences}{traceModeDecreaseIndent} PHASE 1: in ALIGNMENT BLOCK environment, looking for $masterIndentationArrayOfHashes[-1]{end}\n" if($tracingMode);
-    } elsif($inpreamble and !$inFileContents) {
-        print $logfile "Line $lineCounter\t In preamble, looking for \\begin{document}\n" if($tracingMode);
-    } elsif($inpreamble and $inFileContents) {
-        print $logfile "Line $lineCounter\t In preamble, in filecontents environment\n" if($tracingMode);
-    } else {
-        print $logfile "Line $lineCounter\t $masterSettings{logFilePreferences}{traceModeDecreaseIndent} PHASE 1: looking for reasons to DECREASE indentation of CURRENT line \n" if($tracingMode);
-    }
-
-    # check to see if we have \end{something} or \]
-    &at_end_of_env_or_eq() unless ($inpreamble or $inIndentBlock);
-
-    # check to see if we have %* \end{something} for alignment blocks
-    # outside of environments
-    &end_command_with_alignment();
-
-    # check to see if we're at the end of a noindent
-    # block %\end{noindent}
-    &at_end_noindent();
-
-    # only check for unmatched braces if we're not in
-    # a verbatim-like environment or in the preamble or in a
-    # noIndentBlock or in a delimiter block
-    if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters)) {
-        # The check for closing } and ] relies on counting, so
-        # we have to remove trailing comments so that any {, }, [, ]
-        # that are found after % are not counted
-        #
-        # note that these lines are NOT in @lines, so we
-        # have to store the $trailingcomments to put
-        # back on after the counting
-        #
-        # note the use of (?<!\\)% so that we don't match \%
-        if ( $_=~ m/(?<!\\)%.*/) {
-            s/((?<!\\)%.*)//;
-            $trailingcomments=$1;
-
-            # tracing mode
-            print $logfile "Line $lineCounter\t Removed trailing comments to count braces and brackets: $1\n" if($tracingMode);
-        }
-
-        # check to see if we're at the end of a \parbox, \marginpar
-        # or other split-across-lines command and check that
-        # we're not starting another command that has split braces (nesting)
-        &end_command_or_key_unmatched_braces();
-
-        # check to see if we're at the end of a command that splits
-        # [ ] across lines
-        &end_command_or_key_unmatched_brackets();
-
-        # check for a heading such as \chapter, \section, etc
-        &indent_heading();
-
-        # check for \item
-        &indent_item();
-
-        # check for \else or \fi
-        &indent_if_else_fi();
-
-        # add the trailing comments back to the end of the line
-        if(scalar($trailingcomments)) {
-            # some line break magic, http://stackoverflow.com/questions/881779/neatest-way-to-remove-linebreaks-in-perl
-            s/\R//;
-            $_ = $_ . $trailingcomments."\n" ;
-
-            # tracing mode
-            print $logfile "Line $lineCounter\t counting braces/brackets complete\n" if($tracingMode);
-            print $logfile "Line $lineCounter\t Adding trailing comments back on: $trailingcomments\n" if($tracingMode);
-
-            # empty the trailingcomments
-            $trailingcomments='';
-
-        }
-        # remove trailing whitespace
-        if ($removeTrailingWhitespace) {
-            print $logfile "Line $lineCounter\t removing trailing whitespace (see removeTrailingWhitespace)\n" if ($tracingMode);
-            s/\s+$/\n/;
-        }
-    }
-
-    # ADD CURRENT LEVEL OF INDENTATION
-    # ADD CURRENT LEVEL OF INDENTATION
-    # ADD CURRENT LEVEL OF INDENTATION
-    # (unless we're in a delimiter-aligned block)
-    if(!$delimiters) {
-        # make sure we're not in a verbatim block or in the preamble
-        if($inverbatim or $inpreamble or $inIndentBlock) {
-           # just push the current line as is
-           push(@lines,$_);
-        } else {
-            # add current value of indentation to the current line
-            # and output it
-            # unless this would only create trailing whitespace and the
-            # corresponding option is set
-            unless ($_ =~ m/^$/ and $removeTrailingWhitespace){
-                $_ = &current_indentation().$_;
-            }
-            push(@lines,$_);
-            # tracing mode
-            print $logfile "Line $lineCounter\t $masterSettings{logFilePreferences}{traceModeAddCurrentIndent} PHASE 2: Adding current level of indentation: ",&current_indentation_names(),"\n" if($tracingMode);
-        }
-    } else {
-        # output to @block (within masterIndentationArrayOfHashes) if we're in a delimiter block
-        push(@{$masterIndentationArrayOfHashes[-1]{block}},$_);
-
-        # tracing mode
-        print $logfile "Line $lineCounter\t In delimeter block ($masterIndentationArrayOfHashes[-1]{name}), waiting for block formatting\n" if($tracingMode);
-    }
-
-    # \BEGIN{ENVIRONMENT} or OPEN { or OPEN [
-    # \BEGIN{ENVIRONMENT} or OPEN { or OPEN [
-    # \BEGIN{ENVIRONMENT} or OPEN { or OPEN [
-
-    # check to see if we're beginning a filecontents environment
-    if( ($_ =~ m/^\s*\\begin\{(.*?)\}/ and  $fileContentsEnvironments{$1} and !$inverbatim)){
-        print $logfile "Line $lineCounter\t Found filecontents environment (see fileContentsEnvironments)\n" if($tracingMode);
-        $inFileContents = 1;
-    }
-
-    # only check for new environments or commands if we're
-    # not in a verbatim-like environment or in the preamble
-    # or in a noIndentBlock, or delimiter block
-    if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters)) {
-
-        print $logfile "Line $lineCounter\t $masterSettings{logFilePreferences}{traceModeIncreaseIndent} PHASE 3: looking for reasons to INCREASE indentation of SUBSEQUENT lines \n" if($tracingMode);
-
-        # check if we are in a
-        #   % \begin{noindent}
-        # block; this is similar to a verbatim block, the user
-        # may not want some blocks of code to be touched
-        #
-        # IMPORTANT: this needs to go before the trailing comments
-        # are removed!
-        &at_beg_noindent();
-
-        # check for
-        #   %* \begin{tabular}
-        # which might be used to align blocks that contain delimeters that
-        # are NOT contained in an alignment block in the usual way, e.g
-        #   \matrix{
-        #       %* \begin{tabular}
-        #           1 & 2 \\
-        #           3 & 4 \\
-        #       %* \end{tabular}
-        #           }
-        &begin_command_with_alignment();
-        if(@masterIndentationArrayOfHashes){
-               $delimiters = $masterIndentationArrayOfHashes[-1]{alignmentDelimiters}||0;
-             }
-
-        # remove trailing comments so that any {, }, [, ]
-        # that are found after % are not counted
-        #
-        # note that these lines are already in @lines, so we
-        # can remove the trailing comments WITHOUT having
-        # to put them back in
-        #
-        # Note that this won't match \%
-        s/(?<!\\)%.*// if( $_=~ m/(?<!\\)%.*/);
-
-        # tracing mode
-        print $logfile "Line $lineCounter\t Removing trailing comments for brace count (line is already stored)\n" if($tracingMode);
-
-        # check to see if we have \begin{something} or \[
-        &at_beg_of_env_or_eq() if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters));
-        if(@masterIndentationArrayOfHashes){
-               $delimiters = $masterIndentationArrayOfHashes[-1]{alignmentDelimiters}||0;
-             }
-
-        # check to see if we have \parbox, \marginpar, or
-        # something similar that might split braces {} across lines,
-        # specified in %checkunmatched hash table
-        &start_command_or_key_unmatched_braces() if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters));
-
-        # check for an else statement (braces, not \else)
-        &check_for_else() if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters));
-
-        # check for a command that splits [] across lines
-        &start_command_or_key_unmatched_brackets();
-
-        # check for a heading
-        &indent_after_heading() if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters));
-
-        # check for \item
-        &indent_after_item() if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters));
-
-        # check for \if or \else command
-        &indent_after_if_else_fi() if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters));
-
-        # tracing mode
-        if($tracingMode){
-            if(scalar(@masterIndentationArrayOfHashes)){
-                print $logfile "Line $lineCounter\t Indentation array: ",&current_indentation_names(),"\n";
-              } else {
-                print $logfile "Line $lineCounter\t Indentation array empty\n";
-              }
-        }
-    }
-}
-
-# close the main file
-close(MAINFILE);
-
-# put line count information in the log file
-print $logfile "Line Count of $fileName: ",scalar(@mainfile),"\n";
-print $logfile "Line Count of indented $fileName: ",scalar(@lines);
-if(scalar(@mainfile) != scalar(@lines))
-{
-  print $logfile <<ENDQUOTE
-WARNING: \t line count of original file and indented file does
-\t not match- consider reverting to a back up, see $backupExtension;
-ENDQUOTE
-;
-} else {
-    print $logfile "\n\nLine counts of original file and indented file match.\n";
-}
-
-# output the formatted lines to the terminal
-print @lines if(!$silentMode);
-
-# if -w is active then output to $ARGV[0]
-if($overwrite) {
-    open(OUTPUTFILE,">",$fileName);
-    print OUTPUTFILE @lines;
-    close(OUTPUTFILE);
-}
-
-# if -o is active then output to $ARGV[1]
-if($outputToFile) {
-    open(OUTPUTFILE,">",$ARGV[1]);
-    print OUTPUTFILE @lines;
-    close(OUTPUTFILE);
-    print $logfile "Output from indentation written to $ARGV[1].\n";
-}
-
-# final line of the logfil
-print $logfile "\n",$masterSettings{logFilePreferences}{endLogFileWith};
-
-# close the log file
-close($logfile);
-
+my $document = LatexIndent::Document->new(name=>"masterdocument",fileName=>$ARGV[0],switches=>\%switches);
+$document->latexindent;
 exit(0);
-
-sub indent_if_else_fi{
-    # PURPOSE: set indentation of line that contains \else, \fi  command
-    #
-    #
-
-    # @masterIndentationArrayOfHashes could be empty -- if so, exit
-    return unless @masterIndentationArrayOfHashes;
-    return unless $constructIfElseFi{$masterIndentationArrayOfHashes[-1]{name}};
-
-    # look for \fi
-    if( $_ =~ m/^\s*\\fi/) {
-        # tracing mode
-        print $logfile "Line $lineCounter\t \\fi command found, matching: \\",$masterIndentationArrayOfHashes[-1]{name}, "\n" if($tracingMode);
-        &decrease_indent($masterIndentationArrayOfHashes[-1]{name});
-    } 
-    # look for \else or \or
-    elsif( $_ =~ m/^\s*\\else/ or $_ =~ m/^\s*\\or/ ) {
-        # tracing mode
-        print $logfile "Line $lineCounter\t \\else command found, matching: \\",$masterIndentationArrayOfHashes[-1]{name}, "\n" if($tracingMode);
-        print $logfile "Line $lineCounter\t decreasing indent, still looking for \\fi to match \\",&current_indentation_names(), "\n" if($tracingMode);
-
-        # finding an \else or \or command removes the *indentation*, but not the entry from the master hash
-        $masterIndentationArrayOfHashes[-1]{indent}="";
-    }
-}
-
-sub indent_after_if_else_fi{
-    # PURPOSE: set indentation *after* \if construct such as
-    #
-    #               \ifnum\x=2
-    #                   <stuff>
-    #                   <stuff>
-    #               \else
-    #                   <stuff>
-    #                   <stuff>
-    #               \fi
-    #
-    #   How to read /^\s*\\(if.*?)(\s|\\|\#)
-    #
-    #       ^\s*        begins with multiple spaces (possibly none)
-    #       \\(if.*?)(\s|\\|\#)   matches \if... up to either a
-    #                             space, a \, or a #
-    #   Note: this won't match \if.*\fi
-    if( $_ =~ m/^\s*\\(if.*?)(\s|\\|\#)/ and $_ !~ m/^\s*\\(if.*?\\fi)/ and $constructIfElseFi{$1}) {
-        # tracing mode
-        print $logfile "Line $lineCounter\t ifelsefi construct found: $1 \n" if($tracingMode);
-        &increase_indent({name=>$1,type=>"ifelseif"});
-    } elsif(@masterIndentationArrayOfHashes) {
-        if( ($_ =~ m/^\s*\\else/ or $_ =~ m/^\s*\\or/ ) and $constructIfElseFi{$masterIndentationArrayOfHashes[-1]{name}}) {
-            # tracing mode
-            print $logfile "Line $lineCounter\t setting indent *after* \\else or \\or command found for $masterIndentationArrayOfHashes[-1]{name} \n" if($tracingMode);
-
-            # recover the indentation to be implemented *after* the \else or \or
-            $masterIndentationArrayOfHashes[-1]{indent}=$indentRules{$masterIndentationArrayOfHashes[-1]{name}}||$defaultIndent unless ($noAdditionalIndent{$masterIndentationArrayOfHashes[-1]{name}});
-        }
-  }
-}
-
-sub indent_item{
-    # PURPOSE: when considering environments that can contain items, such 
-    #          as enumerate, itemize, etc, this subroutine sets the indentation for the item *itself*
-
-    return unless(scalar(@masterIndentationArrayOfHashes)>1);
-    return unless $indentAfterItems{$masterIndentationArrayOfHashes[-2]{name}};
-
-    if( $_ =~ m/^\s*\\(.*?)(\[|\s)/ and $itemNames{$1}){
-        # tracing mode
-        print $logfile "Line $lineCounter\t $1 found within ",$masterIndentationArrayOfHashes[-1]{name}," environment (see indentAfterItems and itemNames)\n" if($tracingMode);
-        if($itemNames{$masterIndentationArrayOfHashes[-1]{name}}) {
-            print $logfile "Line $lineCounter\t $1 found - neutralizing indentation from previous ",$masterIndentationArrayOfHashes[-1]{name},"\n" if($tracingMode);
-            &decrease_indent($1);
-        }
-    }
-
-}
-
-sub indent_after_item{
-    # PURPOSE: Set the indentation *after* the item
-    #          This matches a line that begins with
-    #
-    #               \item
-    #               \item[
-    #               \myitem
-    #               \myitem[
-    #
-    #           or anything else specified in itemNames
-    #
-    return unless @masterIndentationArrayOfHashes;
-    return unless $indentAfterItems{$masterIndentationArrayOfHashes[-1]{name}};
-
-    if( $_ =~ m/^\s*\\(.*?)(\[|\s)/
-            and $itemNames{$1}) {
-        # tracing mode
-        print $logfile "Line $lineCounter\t $1 found within ",$masterIndentationArrayOfHashes[-1]{name}," environment (see indentAfterItems and itemNames)\n" if($tracingMode);
-        &increase_indent({name=>$1,type=>"item"});
-    }
-}
-
-sub begin_command_with_alignment{
-    # PURPOSE: This matches
-    #           %* \begin{tabular}
-    #          with any number of spaces (possibly none) between
-    #          the * and \begin{noindent}.
-    #
-    #          the comment symbol IS indended!
-    #
-    #          This is to align blocks that contain delimeters that
-    #          are NOT contained in an alignment block in the usual way, e.g
-    #             \matrix{
-    #                 %* \begin{tabular}
-    #                     1 & 2 \\
-    #                     3 & 4 \\
-    #                 %* \end{tabular}
-    #                     }
-
-    if( $_ =~ m/^\s*%\*\s*\\begin\{(.*?)\}/ and $lookForAlignDelims{$1}) {
-           # increase the indentation
-           &increase_indent({name=>$1,
-                             alignmentDelimiters=>1,
-                             type=>"environment",
-                             begin=>"\\begin{$1}",
-                             end=>"\\end{$1}"});
-           # tracing mode
-           print $logfile "Line $lineCounter\t Delimiter environment started: $1 (see lookForAlignDelims)\n" if($tracingMode);
-    }
-}
-
-sub end_command_with_alignment{
-    # PURPOSE: This matches
-    #           %* \end{tabular}
-    #          with any number of spaces (possibly none) between
-    #          the * and \end{tabular} (or any other name used from
-    #          lookFroAlignDelims)
-    #
-    #          Note: the comment symbol IS indended!
-    #
-    #          This is to align blocks that contain delimeters that
-    #          are NOT contained in an alignment block in the usual way, e.g
-    #             \matrix{
-    #                 %* \begin{tabular}
-    #                     1 & 2 \\
-    #                     3 & 4 \\
-    #                 %* \end{tabular}
-    #                     }
-    return unless @masterIndentationArrayOfHashes;
-    return unless $masterIndentationArrayOfHashes[-1]{alignmentDelimiters};
-
-    if( $_ =~ m/^\s*%\*\s*\\end\{(.*?)\}/ and $lookForAlignDelims{$1}) {
-        # same subroutine used at the end of regular tabular, align, etc
-        # environments
-        if($delimiters) {
-            &print_aligned_block();
-            &decrease_indent($1);
-        } else {
-            # tracing mode
-            print $logfile "Line $lineCounter\t FYI: did you mean to start a delimiter block on a previous line? \n" if($tracingMode);
-            print $logfile "Line $lineCounter\t      perhaps using %* \\begin{$1}\n" if($tracingMode);
-        }
-    }
-}
-
-sub indent_heading{
-    # PURPOSE: This matches
-    #           \part
-    #           \chapter
-    #           \section
-    #           \subsection
-    #           \subsubsection
-    #           \paragraph
-    #           \subparagraph
-    #
-    #           and anything else listed in indentAfterHeadings
-    #
-    #           This subroutine specifies the indentation for the
-    #           heading itself, i.e the line that has \chapter, \section etc
-    if( $_ =~ m/^\s*\\(.*?)(\[|{)/ and $indentAfterHeadings{$1}){
-       # tracing mode
-       print $logfile "Line $lineCounter\t Heading found: $1 \n" if($tracingMode);
-
-       # get the heading settings, it's a hash within a hash
-       my %currentHeading = %{$indentAfterHeadings{$1}};
-
-       # $previousHeadingLevel: scalar that stores which heading
-       # we are under: \part, \chapter, etc
-       my $previousHeadingLevel=0;         
-
-       # form an array of the headings available
-       my @headingStore=();
-       foreach my $env (@masterIndentationArrayOfHashes){
-           if($env->{type} eq 'heading'){
-               push(@headingStore,$env->{name});
-               # update heading level
-               $previousHeadingLevel= $env->{headinglevel};
-             }
-         }
-
-       # if current heading level < old heading level,
-       if($currentHeading{level}<$previousHeadingLevel) {
-            # decrease indentation, but only if
-            # specified in indentHeadings. Note that this check
-            # needs to be done here- decrease_indent won't
-            # check a nested hash
-
-            if(scalar(@headingStore)) {
-               while($currentHeading{level}<$previousHeadingLevel and scalar(@headingStore)) {
-                    my $higherHeadingName = pop(@headingStore);
-                    my %higherLevelHeading = %{$indentAfterHeadings{$higherHeadingName}};
-
-                    # tracing mode
-                    print $logfile "Line $lineCounter\t stepping UP heading level from $higherHeadingName \n" if($tracingMode);
-
-                    &decrease_indent($higherHeadingName) if($higherLevelHeading{indent});
-                    $previousHeadingLevel=$higherLevelHeading{level};
-               }
-               # put the heading name back in to storage
-               push(@headingStore,$1);
-            }
-       } elsif($currentHeading{level}==$previousHeadingLevel) {
-            if(scalar(@headingStore)) {
-                 my $higherHeadingName = pop(@headingStore);
-                 my %higherLevelHeading = %{$indentAfterHeadings{$higherHeadingName}};
-                 &decrease_indent($higherHeadingName) if($higherLevelHeading{indent});
-            }
-       } 
-    }
-}
-
-sub indent_after_heading{
-    # PURPOSE: This matches
-    #           \part
-    #           \chapter
-    #           \section
-    #           \subsection
-    #           \subsubsection
-    #           \paragraph
-    #           \subparagraph
-    #
-    #           and anything else listed in indentAfterHeadings
-    #
-    #           This subroutine is specifies the indentation for
-    #           the text AFTER the heading, i.e the body of conent
-    #           in each \chapter, \section, etc
-    if( $_ =~ m/^\s*\\(.*?)(\[|{)/ and $indentAfterHeadings{$1}) {
-       # get the heading settings- it's a hash within a hash
-       my %currentHeading = %{$indentAfterHeadings{$1}};
-
-       &increase_indent({name=>$1,type=>"heading",headinglevel=>$currentHeading{level}}) if($currentHeading{indent});
-    }
-}
-
-sub at_end_noindent{
-    # PURPOSE: This matches
-    #           % \end{noindent}
-    #          with any number of spaces (possibly none) between
-    #          the comment and \end{noindent}.
-    #
-    #          the comment symbol IS indended!
-    #
-    #          This is for blocks of code that the user wants
-    #          to leave untouched- similar to verbatim blocks
-
-    if( $_ =~ m/^%\s*\\end\{(.*?)\}/ and $noIndentBlock{$1}) {
-            $inIndentBlock=0;
-            # tracing mode
-            print $logfile "Line $lineCounter\t % \\end{no indent block} found, switching inIndentBlock OFF \n" if($tracingMode);
-    }
-}
-
-sub at_beg_noindent{
-    # PURPOSE: This matches
-    #           % \begin{noindent}
-    #          with any number of spaces (possibly none) between
-    #          the comment and \begin{noindent}.
-    #
-    #          the comment symbol IS indended!
-    #
-    #          This is for blocks of code that the user wants
-    #          to leave untouched- similar to verbatim blocks
-
-    if( $_ =~ m/^%\s*\\begin\{(.*?)\}/ and $noIndentBlock{$1}) {
-           $inIndentBlock = 1;
-           # tracing mode
-           print $logfile "Line $lineCounter\t % \\begin{no indent block} found, switching inIndentBlock ON \n" if($tracingMode);
-    }
-}
-
-sub start_command_or_key_unmatched_brackets{
-    # PURPOSE: This matches
-    #              \pgfplotstablecreatecol[...
-    #
-    #              or any other command/key that has brackets [ ]
-    #              split across lines specified in the
-    #              hash tables, %checkunmatchedbracket
-    #
-    # How to read: ^\s*(\\)?(.*?)(\[\s*)
-    #
-    #       ^       line begins with
-    #       \s*     any (or no)spaces
-    #       (\\)?   matches a \ backslash but not necessarily
-    #       (.*?)   non-greedy character match and store the result
-    #       ((?<!\\)\[\s*) match [ possibly leading with spaces
-    #                      but it WON'T match \[
-
-    if ($_ =~ m/^\s*(\\)?(.*?)(\s*(?<!\\)\[)/
-        and ($checkunmatchedbracket{$2} or $alwaysLookforSplitBrackets)) {
-            # store the command name, because $2
-            # will not exist after the next match
-            my $commandname = $2;
-            my $matchedBRACKETS=0;
-
-            # match [ but don't match \[
-            $matchedBRACKETS++ while ($_ =~ /(?<!\\)\[/g);
-            # match ] but don't match \]
-            $matchedBRACKETS-- while ($_ =~ /(?<!\\)\]/g);
-
-            # set the indentation
-            if($matchedBRACKETS != 0 ) {
-                  # tracing mode
-                  print $logfile "Line $lineCounter\t Found opening BRACKET [ $commandname\n" if($tracingMode);
-
-                  &increase_indent({name=>$commandname,matchedBRACKETS=>$matchedBRACKETS,type=>'splitBrackets'});
-            }
-        }
-}
-
-sub end_command_or_key_unmatched_brackets{
-    # PURPOSE:  Check for the closing BRACKET of a command that
-    #           splits its BRACKETS across lines, such as
-    #
-    #               \pgfplotstablecreatecol[ ...
-    #
-    #           It works by checking if we have any entries
-    #           in the array @masterIndentationArrayOfHashes, and making
-    #           sure that we're not starting another command/key
-    #           that has split BRACKETS (nesting).
-    #
-    #           It also checks that the line is not commented.
-    #
-    #           We count the number of [ and ADD to the counter
-    #                                  ] and SUBTRACT to the counter
-    return unless @masterIndentationArrayOfHashes;
-    return unless ($masterIndentationArrayOfHashes[-1]{type} eq 'splitBrackets');
-    print $logfile "Line $lineCounter\t Searching for closing BRACKET ] $masterIndentationArrayOfHashes[-1]{name}\n" if($tracingMode);
-
-    if(!($_ =~ m/^\s*(\\)?(.*?)(\s*\[)/
-        and ($checkunmatchedbracket{$2} or $alwaysLookforSplitBrackets))
-        and $_ !~ m/^\s*%/) {
-
-       # get the details of the most recent command name
-       my $commandname =  $masterIndentationArrayOfHashes[-1]{name};
-       my $matchedBRACKETS = $masterIndentationArrayOfHashes[-1]{matchedBRACKETS};
-
-       # match [ but don't match \[
-       $matchedBRACKETS++ while ($_ =~ m/(?<!\\)\[/g);
-
-       # match ] but don't match \]
-       $matchedBRACKETS-- while ($_ =~ m/(?<!\\)\]/g);
-
-       # if we've matched up the BRACKETS then
-       # we can decrease the indent by 1 level
-       if($matchedBRACKETS == 0){
-            # tracing mode
-            print $logfile "Line $lineCounter\t Found closing BRACKET ] $commandname\n" if($tracingMode);
-
-            # decrease the indentation (if appropriate)
-            &decrease_indent($commandname);
-       } else {
-           # otherwise we need to enter the new value
-           # of $matchedBRACKETS and the value of $command
-           # back into storage
-           $masterIndentationArrayOfHashes[-1]{matchedBRACKETS} = $matchedBRACKETS;
-
-           # tracing mode
-           print $logfile "Line $lineCounter\t Searching for closing BRACKET ] $commandname\n" if($tracingMode);
-       }
-     }
-}
-
-sub start_command_or_key_unmatched_braces{
-    # PURPOSE: This matches
-    #              \parbox{...
-    #              \parbox[..]..{
-    #              empty header/.style={
-    #              \foreach \something
-    #              etc
-    #
-    #              or any other command/key that has BRACES
-    #              split across lines specified in the
-    #              hash tables, %checkunmatched, %checkunmatchedELSE
-    #
-    # How to read: ^\s*(\\)?(.*?)(\[|{|\s)
-    #
-    #       ^                  line begins with
-    #       \s*                any (or no) spaces
-    #       (\\)?              matches a \ backslash but not necessarily
-    #       (.*?)              non-greedy character match and store the result
-    #       (\[|}|=|(\s*\\))   either [ or { or = or space \
-
-    if ($_ =~ m/^\s*(\\)?(.*?)(\[|{|=|(\s*\\))/
-            and ($checkunmatched{$2} or $checkunmatchedELSE{$2}
-                 or $alwaysLookforSplitBraces)
-        ) {
-            # store the command name, because $2
-            # will not exist after the next match
-            my $commandname = $2;
-            my $matchedbraces=0;
-
-            # by default, don't look for an else construct
-            my $lookforelse=$checkunmatchedELSE{$2}||0;
-
-            # match { but don't match \{
-            $matchedbraces++ while ($_ =~ /(?<!\\){/g);
-
-            # match } but don't match \}
-            $matchedbraces-- while ($_ =~ /(?<!\\)}/g);
-
-            # tracing mode
-            print $logfile "Line $lineCounter\t matchedbraces = $matchedbraces\n" if($tracingMode);
-
-            # set the indentation
-            if($matchedbraces > 0 ) {
-                  # tracing mode
-                  print $logfile "Line $lineCounter\t Found opening BRACE { $commandname\n" if($tracingMode);
-
-                  &increase_indent({name=>$commandname,
-                                      matchedbraces=>$matchedbraces,
-                                      lookforelse=>$lookforelse,
-                                      countzeros=>0,
-                                      type=>"splitbraces"});
-            } elsif($matchedbraces<0) {
-                # if $matchedbraces < 0 then we must be matching
-                # braces from a previous split-braces command
-
-                # keep matching { OR }, and don't match \{ or \}
-                while ($_ =~ m/(((?<!\\){)|((?<!\\)}))/g) {
-
-                     # store the match, either { or }
-                     my $braceType = $1;
-
-                     # exit the loop if @masterIndentationArrayOfHashes[-1] is empty
-                     last if(!@masterIndentationArrayOfHashes);
-
-                     # exit the loop if we're not looking for split braces
-                     last if($masterIndentationArrayOfHashes[-1]{type} ne 'splitbraces');
-
-                     # get the details of the most recent command name
-                     $commandname =  $masterIndentationArrayOfHashes[-1]{name};
-                     $matchedbraces = $masterIndentationArrayOfHashes[-1]{'matchedbraces'};
-                     my $countzeros = $masterIndentationArrayOfHashes[-1]{'countzeros'};
-                     $lookforelse= $masterIndentationArrayOfHashes[-1]{'lookforelse'};
-
-                     $matchedbraces++ if($1 eq "{");
-                     $matchedbraces-- if($1 eq "}");
-
-                     # update the matched braces count
-                     $masterIndentationArrayOfHashes[-1]{matchedbraces} = $matchedbraces;
-
-                     # if we've matched up the braces then
-                     # we can decrease the indent by 1 level
-                     if($matchedbraces == 0) {
-                          $countzeros++ if $lookforelse;
-
-                          # tracing mode
-                          print $logfile "Line $lineCounter\t Found closing BRACE } $1\n" if($tracingMode);
-
-                          # decrease the indentation (if appropriate)
-                          &decrease_indent($commandname);
-
-                         if($countzeros==1) {
-                              $masterIndentationArrayOfHashes[-1]{'matchedbraces'} = $matchedbraces;
-                              $masterIndentationArrayOfHashes[-1]{'countzeros'} = $countzeros;
-                              $masterIndentationArrayOfHashes[-1]{'lookforelse'} = $lookforelse;
-                         }
-                     } 
-                }
-            }
-        }
-}
-
-sub end_command_or_key_unmatched_braces{
-    # PURPOSE:  Check for the closing BRACE of a command that
-    #           splits its BRACES across lines, such as
-    #
-    #               \parbox{ ...
-    #
-    #           or one of the tikz keys, such as
-    #
-    #              empty header/.style={
-    #
-    #           It works by checking if we have any entries
-    #           in the array @masterIndentationArrayOfHashes, and making
-    #           sure that we're not starting another command/key
-    #           that has split BRACES (nesting).
-    #
-    #           It also checks that the line is not commented.
-    #
-    #           We count the number of { and ADD to the counter
-    #                                  } and SUBTRACT to the counter
-    return unless @masterIndentationArrayOfHashes;
-    return unless ($masterIndentationArrayOfHashes[-1]{type} eq 'splitbraces');
-    print $logfile "Line $lineCounter\t Searching for closing BRACE } $masterIndentationArrayOfHashes[-1]{name}\n" if($tracingMode);
-
-    if(!($_ =~ m/^\s*(\\)?(.*?)(\[|{|=|(\s*\\))/
-        and ($checkunmatched{$2} or $checkunmatchedELSE{$2} or $alwaysLookforSplitBraces))
-        and $_ !~ m/^\s*%/
-       ) {
-       # keep matching { OR }, and don't match \{ or \}
-       while ($_ =~ m/(((?<!\\){)|((?<!\\)}))/g) {
-            # store the match, either { or }
-            my $braceType = $1;
-
-            # exit the loop if @masterIndentationArrayOfHashes[-1] is empty
-            last if(!@masterIndentationArrayOfHashes);
-
-            # exit the loop if we're not looking for split braces
-            last if($masterIndentationArrayOfHashes[-1]{type} ne 'splitbraces');
-
-            # get the details of the most recent command name
-            my $commandname =  $masterIndentationArrayOfHashes[-1]{name};
-            my $matchedbraces = $masterIndentationArrayOfHashes[-1]{matchedbraces};
-            my $countzeros = $masterIndentationArrayOfHashes[-1]{countzeros};
-            my $lookforelse= $masterIndentationArrayOfHashes[-1]{lookforelse};
-
-            $matchedbraces++ if($1 eq "{");
-            $matchedbraces-- if($1 eq "}");
-
-            # update the matched braces count
-            $masterIndentationArrayOfHashes[-1]{matchedbraces} = $matchedbraces;
-
-            # if we've matched up the braces then
-            # we can decrease the indent by 1 level
-            if($matchedbraces == 0) {
-                 $countzeros++ if $lookforelse;
-
-                 # tracing mode
-                 print $logfile "Line $lineCounter\t Found closing BRACE } $commandname\n" if($tracingMode);
-
-                 # decrease the indentation (if appropriate)
-                 &decrease_indent($commandname);
-
-                if($countzeros==1){
-                    $masterIndentationArrayOfHashes[-1]{'matchedbraces'} = $matchedbraces;
-                    $masterIndentationArrayOfHashes[-1]{'countzeros'} = $countzeros;
-                    $masterIndentationArrayOfHashes[-1]{'lookforelse'} = $lookforelse;
-                }
-            } 
-            
-            if(@masterIndentationArrayOfHashes){
-                if($masterIndentationArrayOfHashes[-1]{'type'} eq 'splitbraces'){
-                   # tracing mode
-                   print $logfile "Line $lineCounter\t Searching for closing BRACE } $masterIndentationArrayOfHashes[-1]{name}\n" if($tracingMode);
-                }
-             }
-        }
-     }
-}
-
-sub check_for_else{
-    # PURPOSE: Check for an else clause
-    #
-    #          Some commands have the form
-    #
-    #               \mycommand{
-    #                   if this
-    #               }
-    #               {
-    #                   else this
-    #               }
-    #
-    #          so we need to look for the else bit, and set
-    #          the indentation appropriately.
-    #
-    #          We only perform this check if there's something
-    #          in the array @masterIndentationArrayOfHashes, and if
-    #          the line itself is not a command, or comment,
-    #          and if it begins with {
-
-    if(scalar(@masterIndentationArrayOfHashes)
-        and  !($_ =~ m/^\s*(\\)?(.*?)(\[|{|=)/
-                    and ($checkunmatched{$2} or $checkunmatchedELSE{$2}
-                         or $alwaysLookforSplitBraces))
-        and $_ =~ m/^\s*{/
-        and $_ !~ m/^\s*%/
-       ) {
-       # get the details of the most recent command name
-       my $matchedbraces = $masterIndentationArrayOfHashes[-1]{'matchedbraces'};
-       my $countzeros = $masterIndentationArrayOfHashes[-1]{'countzeros'};
-       my $lookforelse= $masterIndentationArrayOfHashes[-1]{'lookforelse'};
-
-       # increase indentation
-       if($lookforelse and $countzeros==1) {
-         #&increase_indent($commandname);
-       }
-
-       # put the array back together
-       $masterIndentationArrayOfHashes[-1]{'matchedbraces'} = $matchedbraces;
-       $masterIndentationArrayOfHashes[-1]{'countzeros'} = $countzeros;
-       $masterIndentationArrayOfHashes[-1]{'lookforelse'} = $lookforelse;
-    }
-}
-
-sub at_beg_of_env_or_eq{
-    # PURPOSE: Check if we're at the BEGINning of an environment
-    #          or at the BEGINning of a displayed equation \[
-    #
-    #          This subroutine checks for matches of the form
-    #
-    #               \begin{environmentname}
-    #          or
-    #               \[
-    #
-    #          It also checks to see if the current environment
-    #          should have alignment delimiters; if so, we need to turn
-    #          ON the $delimiter switch
-
-    # How to read
-    #  m/^\s*(\$)?\\begin{(.*?)}/
-    #
-    #   ^               beginning of a line
-    #   \s*             any white spaces (possibly none)
-    #   (\$)?           possibly a $ symbol, but not required
-    #   \\begin{(.*)?}  \begin{environmentname}
-    #
-    # How to read
-    #  m/^\s*()(\\\[)/
-    #
-    #  ^        beginning of a line
-    #  \s*      any white spaces (possibly none)
-    #  ()       empty just so that $1 and $2 are defined
-    #  (\\\[)   \[  there are lots of \ because both \ and [ need escaping
-    #  \\begin{\\?(.*?)}  \begin{something} where something could start
-    #                     with a backslash, e.g \my@env@ which can happen
-    #                     in a style or class file, for example
-
-    if( (   ( $_ =~ m/^\s*(\$)?\\begin\{\\?(.*?)\}/ and $_ !~ m/\\end\{$2\}/)
-         or ($_=~ m/^\s*()(\\\[)/ and $_ !~ m/\\\]/) )
-        and $_ !~ m/^\s*%/ ) {
-       # tracing mode
-       print $logfile "Line $lineCounter\t \\begin{environment} found: $2 \n" if($tracingMode);
-
-       # increase the indentation
-       &increase_indent({name=>$2,
-                         type=>"environment",
-                         begin=>"\\begin{$2}",
-                         end=>"\\end{$2}"});
-
-       # check for verbatim-like environments
-       if($verbatimEnvironments{$2}){
-           $inverbatim = 1;
-           # tracing mode
-           print $logfile "Line $lineCounter\t \\begin{verbatim-like} found, $2, switching ON verbatim \n" if($tracingMode);
-
-           # remove the key and value from %lookForAlignDelims hash
-           # to avoid any further confusion
-           if($lookForAlignDelims{$2}) {
-                print $logfile "WARNING\n\t Line $lineCounter\t $2 is in *both* lookForAlignDelims and verbatimEnvironments\n";
-                print $logfile "\t\t\t ignoring lookForAlignDelims and prioritizing verbatimEnvironments\n";
-                print $logfile "\t\t\t Note that you only get this message once per environment\n";
-                delete $lookForAlignDelims{$2};
-           }
-       }
-    }
-}
-
-sub at_end_of_env_or_eq{
-    # PURPOSE: Check if we're at the END of an environment
-    #          or at the END of a displayed equation \]
-    #
-    #          This subroutine checks for matches of the form
-    #
-    #               \end{environmentname}
-    #          or
-    #               \]
-    #
-    #          Note: environmentname can begin with a backslash
-    #                which might happen in a sty or cls file.
-    #
-    #          It also checks to see if the current environment
-    #          had alignment delimiters; if so, we need to turn
-    #          OFF the $delimiter switch
-
-    return unless @masterIndentationArrayOfHashes;
-    print $logfile "Line $lineCounter\t looking for \\end{$masterIndentationArrayOfHashes[-1]{name}} \n" if($tracingMode);
-
-    if( ($_ =~ m/^\s*\\end\{\\?(.*?)\}/ or $_=~ m/^(\\\])/) and $_ !~ m/\s*^%/) {
-       # check if we're at the end of a verbatim-like environment
-       if($verbatimEnvironments{$1}) {
-           $inverbatim = 0;
-            # tracing mode
-
-            print $logfile "Line $lineCounter\t \\end{verbatim-like} found: $1, switching off verbatim \n" if($tracingMode);
-            print $logfile "Line $lineCounter\t removing leading spaces \n" if($tracingMode);
-            #s/^\ *//;
-            s/^\t+// if($_ ne "");
-            s/^\s+// if($_ ne "");
-       }
-
-       # check if we're in an environment that is looking
-       # to indent after each \item
-       if(scalar(@masterIndentationArrayOfHashes) and $itemNames{$masterIndentationArrayOfHashes[-1]{name}}) {
-            &decrease_indent($masterIndentationArrayOfHashes[-1]{name});
-       }
-
-       # if we're at the end of an environment that receives no additional indent, log it, and move on
-       if($noAdditionalIndent{$1}){
-            print $logfile "Line $lineCounter\t \\end{$1} finished a no-additional-indent environment (see noAdditionalIndent)\n" if($tracingMode);
-       }
-
-       # some commands contain \end{environmentname}, which
-       # can cause a problem if \begin{environmentname} was not
-       # started previously; if @masterIndentationArrayOfHashes is empty,
-       # then we don't need to check for \end{environmentname}
-       if(@masterIndentationArrayOfHashes) {
-          # check to see if \end{environment} fits with most recent \begin{...}
-          my %previousEnvironment = %{$masterIndentationArrayOfHashes[-1]};
-
-          # check to see if we need to turn off alignment
-          # delimiters and output the current block
-          if($masterIndentationArrayOfHashes[-1]{alignmentDelimiters} and ($previousEnvironment{name} eq $1)) {
-               &print_aligned_block();
-          }
-
-          # tracing mode
-          print $logfile "Line $lineCounter\t \\end{environment} found: $1 \n" if($tracingMode and !$verbatimEnvironments{$1});
-
-          # check to see if \end{environment} fits with most recent \begin{...}
-          if($previousEnvironment{name} eq $1) {
-               # decrease the indentation (if appropriate)
-               print $logfile "Line $lineCounter\t removed $1 from Indentation array\n" if($tracingMode); 
-               &decrease_indent($1);
-          } else {
-              # otherwise put the environment name back on the stack
-              print $logfile "Line $lineCounter\t WARNING: \\end{$1} found on its own line, not matched to \\begin{$previousEnvironment{name}}\n" unless ($delimiters or $inverbatim or $inIndentBlock or $1 eq "\\\]");
-          }
-
-          # need a special check for \[ and \]
-          if($1 eq "\\\]") {
-               &decrease_indent($1);
-          }
-       }
-
-       # if we're at the end of the document, we remove all current
-       # indentation- this is especially prominent in examples that
-       # have headings, and the user has chosen to indentAfterHeadings
-       if($1 eq "document" and !$inFileContents and !$inpreamble and !$delimiters and !$inverbatim and !$inIndentBlock and @masterIndentationArrayOfHashes) {
-            @masterIndentationArrayOfHashes=();
-
-            # tracing mode
-            if($tracingMode) {
-                print $logfile "Line $lineCounter\t \\end{$1} found, emptying indentation array \n" unless ($delimiters or $inverbatim or $inIndentBlock or $1 eq "\\\]");
-            }
-       }
-    }
-}
-
-sub print_aligned_block{
-    # PURPOSE: this subroutine does a few things related
-    #          to printing blocks of code that contain
-    #          delimiters, such as align, tabular, etc
-    #
-    #          It does the following
-    #           - turns off delimiters switch
-    #           - processes the block
-    #           - deletes the block
-    $delimiters=0;
-
-    # tracing mode
-    print $logfile "Line $lineCounter\t Delimiter body FINISHED: $masterIndentationArrayOfHashes[-1]{name}\n" if($tracingMode);
-
-    # print the current FORMATTED block
-    my @block = &format_block(@{$masterIndentationArrayOfHashes[-1]{block}});
-    foreach $line (@block) {
-         # add the indentation and add the
-         # each line of the formatted block
-         # to the output
-         # unless this would only create trailing whitespace and the
-         # corresponding option is set
-         unless ($line =~ m/^$/ and $removeTrailingWhitespace) {
-             $line =&current_indentation().$line;
-         }
-         push(@lines,$line);
-    }
-}
-
-sub format_block{
-    #   PURPOSE: Format a delimited environment such as the
-    #            tabular or align environment that contains &
-    #
-    #   INPUT: @block               array containing unformatted block
-    #                               from, for example, align, or tabular
-    #   OUTPUT: @formattedblock     array containing FORMATTED block
-
-    # @block is the input
-    my @block=@_;
-
-    # tracing mode
-    print $logfile "\t\tFormatting alignment block: $masterIndentationArrayOfHashes[-1]{name}\n" if($tracingMode);
-
-    # step the line counter back to the beginning of the block-
-    # it will be increased back to the end of the block in the
-    # loop later on:  foreach $row (@tmpblock)
-    $lineCounter -= scalar(@block);
-
-    # local array variables
-    my @formattedblock;
-    my @tmprow=();
-    my @tmpblock=();
-    my @maxmstringsize=();
-    my @ampersandCount=();
-
-    # local scalar variables
-    my $alignrowcounter=-1;
-    my $aligncolcounter=-1;
-    my $tmpstring;
-    my $row;
-    my $column;
-    my $maxmcolstrlength;
-    my $i;
-    my $j;
-    my $fmtstring;
-    my $linebreak;
-    my $maxNumberAmpersands = 0;
-    my $currentNumberAmpersands;
-    my $trailingcomments;
-
-    # local hash table
-    my %stringsize=();
-
-    # loop through the block and count & per line- store the biggest
-    # NOTE: this needs to be done in its own block so that
-    # we can know what the maximum number of & in the block is
-    foreach $row (@block) {
-       # delete trailing comments
-       $trailingcomments='';
-       if($row =~ m/((?<!\\)%.*$)/) {
-            $row =~ s/((?<!\\)%.*)/%TC/;
-            $trailingcomments=$1;
-       }
-
-       # reset temporary counter
-       $currentNumberAmpersands=0;
-
-       # count & in current row (exclude \&)
-       $currentNumberAmpersands++ while ($row =~ /(?<!\\)&/g);
-
-       # store the ampersand count for future
-       push(@ampersandCount,$currentNumberAmpersands);
-
-       # overwrite maximum count if the temp count is higher
-       $maxNumberAmpersands = $currentNumberAmpersands if($currentNumberAmpersands > $maxNumberAmpersands );
-
-       # put trailing comments back on
-       if($trailingcomments){
-            $row =~ s/%TC/$trailingcomments/;
-       }
-    }
-
-    # tracing mode
-    print $logfile "\t\tmaximum number of & in any row: $maxNumberAmpersands\n" if($tracingMode);
-
-    # loop through the lines in the @block
-    foreach $row (@block){
-        # get the ampersand count
-        $currentNumberAmpersands = shift(@ampersandCount);
-
-        # increment row counter
-        $alignrowcounter++;
-
-        # clear the $linebreak variable
-        $linebreak='';
-
-        # check for line break \\
-        # and don't mess with a line that doesn't have the maximum
-        # number of &
-        if($row =~ m/\\\\/ and $currentNumberAmpersands==$maxNumberAmpersands ) {
-          # remove \\ and all characters that follow
-          # and put it back in later, once the measurement
-          # has been done
-          $row =~ s/(\\\\.*)//;
-          $linebreak = $1;
-        }
-
-        if($currentNumberAmpersands==$maxNumberAmpersands) {
-
-            # remove trailing comments
-            $trailingcomments='';
-            if($row =~ m/((?<!\\)%.*$)/) {
-                 $row =~ s/((?<!\\)%.*)/%TC/;
-                 $trailingcomments=$1;
-            }
-
-            # separate the row at each &, but not at \&
-            @tmprow = split(/(?<!\\)&/,$row);
-
-            # reset column counter
-            $aligncolcounter=-1;
-
-            # loop through each column element
-            # removing leading and trailing space
-            foreach $column (@tmprow) {
-               # increment column counter
-               $aligncolcounter++;
-
-               # remove leading and trailing space from element
-    	       $column =~ s/^\s+//;
-               $column =~ s/\s+$//;
-
-               # assign string size to the array
-               $stringsize{$alignrowcounter.$aligncolcounter}=length($column);
-               if(length($column)==0){
-                 $column=" ";
-               }
-
-               # put the row back together
-               if ($aligncolcounter ==0){
-                 $tmpstring = $column;
-               } else {
-                 $tmpstring .= "&".$column;
-               }
-            }
-
-
-            # put $linebreak back on the string, now that
-            # the measurement has been done
-            $tmpstring .= $linebreak;
-
-            # put trailing comments back on
-            if($trailingcomments) {
-                 $tmpstring =~ s/%TC/$trailingcomments/;
-            }
-
-            push(@tmpblock,$tmpstring);
-        } else {
-               # if there are no & then use the
-               # NOFORMATTING token
-               # remove leading space
-    	       s/^\s+//;
-               push(@tmpblock,$row."NOFORMATTING");
-        }
-    }
-
-    # calculate the maximum string size of each column
-    for($j=0;$j<=$aligncolcounter;$j++) {
-        $maxmcolstrlength=0;
-        for($i=0; $i<=$alignrowcounter;$i++) {
-            # make sure the stringsize is defined
-            if(defined $stringsize{$i.$j}) {
-                if ($stringsize{$i.$j}>$maxmcolstrlength) {
-                    $maxmcolstrlength = $stringsize{$i.$j};
-                }
-            }
-        }
-        push(@maxmstringsize,$maxmcolstrlength);
-    }
-
-    # README: printf( formatting, expression)
-    #
-    #   formatting has the form %-50s & %-20s & %-19s
-    #   (the numbers have been made up for example)
-    #       the - symbols mean that each column should be left-aligned
-    #       the numbers represent how wide each column is
-    #       the s represents string
-    #       the & needs to be inserted
-
-    # join up the maximum string lengths using "s %-"
-    $fmtstring = join("s & %-",@maxmstringsize);
-
-    # add an s to the end, and a newline
-    $fmtstring .= "s ";
-
-    # add %- to the beginning
-    $fmtstring = "%-".$fmtstring;
-
-    # process the @tmpblock of aligned material
-    foreach $row (@tmpblock) {
-        $linebreak='';
-        # check for line break \\
-        if($row =~ m/\\\\/) {
-          # remove \\ and all characters that follow
-          # and put it back in later
-          $row =~ s/(\\\\.*$)//;
-          $linebreak = $1;
-        }
-
-        if($row =~ m/NOFORMATTING/) {
-            $row =~ s/NOFORMATTING//;
-            $tmpstring=$row;
-
-            # tracing mode
-            print $logfile "\t\tLine $lineCounter\t maximum number of & NOT found- not aligning delimiters \n" if($tracingMode);
-        } else {
-          # remove trailing comments
-          $trailingcomments='';
-          if($row =~ m/((?<!\\)%.*$)/) {
-               $row =~ s/((?<!\\)%.*)/%TC/;
-               $trailingcomments=$1;
-          }
-
-          $tmpstring = sprintf($fmtstring,split(/(?<!\\)&/,$row)).$linebreak."\n";
-
-          # remove space before \\ if specified in alignDoubleBackSlash
-          if($masterIndentationArrayOfHashes[-1]{alignDoubleBackSlash}==0){
-                print $logfile "\t\tLine $lineCounter\t removing space before \\\\ (see $masterIndentationArrayOfHashes[-1]{name} alignDoubleBackSlash)\n" if($tracingMode);
-                $tmpstring =~ s/\s*\\\\/\\\\/;
-                # some users may like to put a number of spaces before \\
-                if($masterIndentationArrayOfHashes[-1]{spacesBeforeDoubleBackSlash}){
-                    my $spaceString;
-                    for($j=1;$j<=$masterIndentationArrayOfHashes[-1]{spacesBeforeDoubleBackSlash};$j++) {
-                        $spaceString .= ' ';
-                    }
-                    print $logfile "\t\tLine $lineCounter\t adding $masterIndentationArrayOfHashes[-1]{spacesBeforeDoubleBackSlash} ",$masterIndentationArrayOfHashes[-1]{spacesBeforeDoubleBackSlash}>1?"spaces":"space"," before \\\\ (see $masterIndentationArrayOfHashes[-1]{name} spacesBeforeDoubleBackSlash)\n" if($tracingMode);
-                    $tmpstring =~ s/\\\\/$spaceString\\\\/;
-                }
-          }
-
-          # put trailing comments back on
-          if($trailingcomments) {
-               $tmpstring =~ s/%TC/$trailingcomments/;
-          }
-
-          # tracing mode
-          print $logfile "\t\tLine $lineCounter\t Found maximum number of & so aligning delimiters\n" if($tracingMode);
-        }
-
-        # remove trailing whitespace
-        if ($removeTrailingWhitespace) {
-            print $logfile "\t\tLine $lineCounter\t removing trailing whitespace from delimiter aligned line\n" if ($tracingMode);
-            $tmpstring =~ s/\s+$/\n/;
-        }
-
-        push(@formattedblock,$tmpstring);
-
-        # increase the line counter
-        $lineCounter++;
-    }
-
-    # return the formatted block
-	@formattedblock;
-}
-
-sub increase_indent{
-       # PURPOSE: Adjust the indentation
-       #          of the current environment, command, etc;
-       #          check that it's not an environment
-       #          that doesn't want indentation.
-
-       my %infoHash = %{pop(@_)};
-       my $command = $infoHash{name};
-
-       # check for conflicting hash keys
-       &check_conflicting_keys($command);
-
-       # quick check for verbatim Environment
-       if($inverbatim){
-            print $logfile "Line $lineCounter\t currently inverbatim environment, not increasing indentation\n" if($tracingMode);
-            return;
-       }
-
-       if($indentRules{$command}) {
-          # tracing mode
-          print $logfile "Line $lineCounter\t increasing indent using rule for $command (see indentRules)\n" if($tracingMode);
-       } else {
-          # default indentation
-          if(!($noAdditionalIndent{$command} or $verbatimEnvironments{$command})) {
-            # tracing mode
-            print $logfile "Line $lineCounter\t increasing indent using defaultIndent\n" if($tracingMode);
-          } elsif($noAdditionalIndent{$command})  {
-            # tracing mode
-            print $logfile "Line $lineCounter\t no additional indent added for $command (see noAdditionalIndent)\n" if($tracingMode);
-          }
-       }
-
-       # add to the master array of hashes
-       push(@masterIndentationArrayOfHashes,\%infoHash);
-
-       # handle the keys slightly different when dealing with environments or commands
-       if($infoHash{type} eq 'environment'){
-            # environments
-            if(!$noAdditionalIndent{$command}){
-                 $masterIndentationArrayOfHashes[-1]{indent} = $indentRules{$command}||$defaultIndent;
-               } 
-            # check to see if we need to look for alignment delimiters
-            if($lookForAlignDelims{$command}){ 
-                # there are two ways to complete the lookForAlignDelims field, either as a scalar
-                # or as a hash, so that we can check for alignDoubleBackSlash. 
-                #
-                # tabular: 
-                #    delims: 1
-                #    alignDoubleBackSlash: 1
-                #
-                # or, simply,
-                #
-                # tabular: 1
-                #
-                # We need to perform a check to see which has been done.
-                if(ref($lookForAlignDelims{$command}) eq 'HASH'){
-                      # tabular: 
-                      #    delims: 1
-                      #    alignDoubleBackSlash: 1
-                      $masterIndentationArrayOfHashes[-1]{alignmentDelimiters}=defined $lookForAlignDelims{$command}{delims}?$lookForAlignDelims{$command}{delims}:1;
-                      $masterIndentationArrayOfHashes[-1]{alignDoubleBackSlash}=defined $lookForAlignDelims{$command}{alignDoubleBackSlash}?$lookForAlignDelims{$command}{alignDoubleBackSlash}:1;
-                      $masterIndentationArrayOfHashes[-1]{spacesBeforeDoubleBackSlash}=$lookForAlignDelims{$command}{spacesBeforeDoubleBackSlash}||0;
-                } else {
-                    # tabular: 1
-                    $masterIndentationArrayOfHashes[-1]{alignmentDelimiters}=1;
-                    $masterIndentationArrayOfHashes[-1]{alignDoubleBackSlash}=1;
-                }
-                if($masterIndentationArrayOfHashes[-1]{alignmentDelimiters}==1){
-                    # tracing mode
-                    print $logfile "Line $lineCounter\t Delimiter environment started: $command (see lookForAlignDelims)\n" if($tracingMode);
-                }
-            }
-       } else {
-            # commands, headings, etc
-            if(!$noAdditionalIndent{$command}){
-                $masterIndentationArrayOfHashes[-1]{indent} = $indentRules{$command}||$defaultIndent;
-             } 
-       }
-
-       # details of noAdditionalIndent to the main hash
-       if($noAdditionalIndent{$command}){
-             $masterIndentationArrayOfHashes[-1]{noAdditionalIndent} = 'yes';
-       }
-}
-
-sub decrease_indent{
-       # PURPOSE: Adjust the indentation
-       #          of the current environment;
-       #          check that it's not an environment
-       #          that doesn't want indentation.
-
-       # if there is no evidence of indentation, then return
-       return unless(scalar(@masterIndentationArrayOfHashes));
-
-       # otherwise get details of the most recent command, environment, item, if, heading, etc
-       my $command = pop(@_);
-
-       if(!$inverbatim) {
-            print $logfile "Line $lineCounter\t removing ", $masterIndentationArrayOfHashes[-1]{name}, " from masterIndentationArrayOfHashes\n" if($tracingMode);
-            pop(@masterIndentationArrayOfHashes);
-            # tracing mode
-            if($tracingMode) {
-                if(@masterIndentationArrayOfHashes) {
-                    print $logfile "Line $lineCounter\t decreasing masterIndentationArrayOfHashes to: ",&current_indentation_names(),"\n";
-                } else {
-                    print $logfile "Line $lineCounter\t masterIndentationArrayOfHashes now empty \n";
-              }
-            }
-       }
-}
-
-sub current_indentation{
-    # PURPOSE: loop through masterIndentationArrayOfHashes and 
-    #          pull out the indentation, and join it together
-
-    # if the masterIndentationArrayOfHashes is empty, return an empty string
-    return "" unless(@masterIndentationArrayOfHashes);
-
-    my $indent;
-    foreach my $env (@masterIndentationArrayOfHashes){
-        $indent .= defined($env->{indent})?$env->{indent}:'';
-      }
-    return $indent;
-}
-
-sub current_indentation_names{
-    # PURPOSE: loop through masterIndentationArrayOfHashes and 
-    #          pull out the list of environment/command names
-    return "masterIndentationArrayOfHashes empty" unless(@masterIndentationArrayOfHashes);
-
-    my $listOfNames;
-    foreach my $env (@masterIndentationArrayOfHashes){
-        $listOfNames .= $env->{name};
-        $listOfNames .= "," unless $env == $masterIndentationArrayOfHashes[-1];
-      }
-    return $listOfNames;
-}
-
-sub check_conflicting_keys{
-  # PURPOSE: users may sometimes put an environment in two
-  #          hash keys; for example, they might put lstlistings
-  #          in both indentRules and in noAdditionalIndent;
-  #          in which case, we need a hierachy.
-  #
-  #          This subroutine implements such a hierachy, 
-  #          and deletes the redundant key.
-
-  # if the user has specified $indentRules{$command} and
-  # $noAdditionalIndent{$command} then they are a bit confused-
-  # we remove the $indentRules{$command} and assume that they
-  # want $noAdditionalIndent{$command}
-
-  my $command = pop(@_);
-
-  if(scalar($indentRules{$command}) and $noAdditionalIndent{$command}) {
-       print $logfile "WARNING\n\t Line $lineCounter\t $command is in *both* indentRules and noAdditionalIndent\n";
-       print $logfile "\t\t\t ignoring indentRules and prioritizing noAdditionalIndent\n";
-       print $logfile "\t\t\t Note that you only get this message once per command/environment\n";
-
-       # remove the key and value from %indentRules hash
-       # to avoid any further confusion
-       delete $indentRules{$command};
-  }
-
-  # if the command is in verbatimEnvironments and in indentRules then
-  # remove it from %indentRules hash
-  # to avoid any further confusion
-  if($indentRules{$command} and $verbatimEnvironments{$command}) {
-       # remove the key and value from %indentRules hash
-       # to avoid any further confusion
-       print $logfile "WARNING\n\t Line $lineCounter\t $command is in *both* indentRules and verbatimEnvironments\n";
-       print $logfile "\t\t\t ignoring indentRules and prioritizing verbatimEnvironments\n";
-       print $logfile "\t\t\t Note that you only get this message once per environment\n";
-       delete $indentRules{$command};
-  }
-
-}