latexindent (5dec14)

git-svn-id: svn://tug.org/texlive/trunk@35757 c570f23f-e606-0410-a88d-b1316a301751

2 files changed, 575 insertions, 198 deletions

diff --git a/Master/texmf-dist/scripts/latexindent/defaultSettings.yaml b/Master/texmf-dist/scripts/latexindent/defaultSettings.yaml
index 457629ce863..799c081f4dc 100755
--- a/Master/texmf-dist/scripts/latexindent/defaultSettings.yaml
+++ b/Master/texmf-dist/scripts/latexindent/defaultSettings.yaml
@@ -34,6 +34,18 @@ onlyOneBackUp: 0
 # many backups are possible, unless onlyOneBackUp is switched on
 maxNumberOfBackUps: 0
 
+# some users may wish to cycle through back up files, for example, 
+# with maxNumberOfBackUps: 4, they may wish to delete the oldest
+# back up file, and keep only the most recent.
+#
+#    copy myfile.bak1 to myfile.bak0
+#    copy myfile.bak2 to myfile.bak1
+#    copy myfile.bak3 to myfile.bak2
+#    copy myfile.bak4 to myfile.bak3
+#
+# the back up will be written to myfile.bak4
+cycleThroughBackUps: 0
+
 # indent preamble
 indentPreamble: 0
 
@@ -53,6 +65,7 @@ removeTrailingWhitespace: 0
 lookForAlignDelims:
    tabular: 1
    tabularx: 1
+   longtable: 1
    array: 1
    matrix: 1
    bmatrix: 1
@@ -64,7 +77,6 @@ lookForAlignDelims:
    aligned: 1
    cases: 1
    dcases: 1
-   pmatrix: 1
    listabla: 1
 
 # if you have indent rules for particular environments
@@ -75,6 +87,7 @@ indentRules:
    anotherenvironment: "\t\t\t\t"
    chapter: " "
    section: " "
+   item: "      "
 
 #  verbatim environments- environments specified 
 #  in this hash table will not be changed at all!
@@ -143,6 +156,53 @@ indentAfterHeadings:
        indent: 0
        level: 7
 
+# if you want the script to look for \item commands 
+# and format it, as follows (for example),
+#       \begin{itemize}
+#           \item content here
+#                 next line is indented
+#                 next line is indented
+#           \item another item
+#       \end{itemize}
+# then populate indentAfterItems. See also itemNames
+indentAfterItems:
+    itemize: 1
+    enumerate: 1
+    list: 1
+
+# if you want to use other names for your items (such as, for example, part)
+# then populate them here- note that you can trick latexindent.pl
+# into indenting all kinds of commands (within environments specified in 
+# indentAfterItems) using this technique.
+itemNames:
+    item: 1
+    myitem: 1
+
+# if you want to indent if, else, fi constructs such as, for example,
+#
+#       \ifnum#1=2
+#               something
+#       \else
+#               something else
+#       \fi
+#
+# then populate them in constructIfElseFi
+constructIfElseFi:
+    ifnum: 1
+    ifdim: 1
+    ifodd: 1
+    ifvmode: 1
+    ifhmode: 1
+    ifmmode: 1
+    ifinner: 1
+    if: 1
+    ifcat: 1
+    ifx: 1
+    ifvoid: 1
+    ifeof: 1
+    iftrue: 1
+    ifcase: 1
+    
 # *** NOTE ***
 # If you have specified alwaysLookforSplitBraces: 1
 # and alwaysLookforSplitBrackets: 1 then you don't need
diff --git a/Master/texmf-dist/scripts/latexindent/latexindent.pl b/Master/texmf-dist/scripts/latexindent/latexindent.pl
index 9376117c324..d023ef014d0 100755
--- a/Master/texmf-dist/scripts/latexindent/latexindent.pl
+++ b/Master/texmf-dist/scripts/latexindent/latexindent.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #	This program is free software: you can redistribute it and/or modify
 #	it under the terms of the GNU General Public License as published by
 #	the Free Software Foundation, either version 3 of the License, or
@@ -13,14 +13,29 @@
 #
 #	For details of how to use this file, please see readme.txt
 
-# load packages/modules
+# load packages/modules: assume strict and warnings are part of every perl distribution
 use strict;
-use warnings;           
-use FindBin;            # help find defaultSettings.yaml 
-use YAML::Tiny;         # interpret defaultSettings.yaml
+use warnings;
+
+# check the other modules are available
+foreach my $moduleName ('FindBin','YAML::Tiny','File::Copy','File::Basename','Getopt::Long','File::HomeDir')
+{
+    # 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::Std;        
 use Getopt::Long;       # to get the switches/options/flags
 use File::HomeDir;      # to get users home directory, regardless of OS
 
@@ -32,7 +47,7 @@ my $tracingMode;
 my $readLocalSettings;
 my $onlyDefault;
 my $showhelp;
-my $cruftDirectory='./';
+my $cruftDirectory;
 
 GetOptions ("w"=>\$overwrite,
 "o"=>\$outputToFile,
@@ -44,12 +59,10 @@ GetOptions ("w"=>\$overwrite,
 "c=s"=>\$cruftDirectory,
 );
 
-die "Could not find directory $cruftDirectory\nExiting, no indentation done." if(!(-d $cruftDirectory));
-
 # version number
-my $versionNumber = "1.11R";
+my $versionNumber = "2.0R";
 
-# Check the number of input arguments- if it is 0 then simply 
+# 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)
 {
@@ -70,6 +83,11 @@ 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 $logfile;
@@ -97,12 +115,12 @@ ENDQUOTE
 # a quick options check
 if($outputToFile and $overwrite)
 {
-    print $logfile <<ENDQUOTE 
+    print $logfile <<ENDQUOTE
 
-WARNING: 
+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;
@@ -115,7 +133,7 @@ if(scalar(@ARGV)>2)
 
 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 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
@@ -144,7 +162,7 @@ ENDQUOTE
     exit(2);
 }
 
-# if the script is called with the -o switch, then check that 
+# 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)
@@ -173,9 +191,9 @@ $defaultSettings = YAML::Tiny->read( "$FindBin::RealBin/defaultSettings.yaml" );
 if(!$defaultSettings)
 {
   for my $fh ($out,$logfile) {
- print $fh <<ENDQUOTE 
+ 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.plx
+        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.
@@ -195,6 +213,7 @@ my $indentPreamble = $defaultSettings->[0]->{indentPreamble};
 my $onlyOneBackUp = $defaultSettings->[0]->{onlyOneBackUp};
 my $maxNumberOfBackUps = $defaultSettings->[0]->{maxNumberOfBackUps};
 my $removeTrailingWhitespace = $defaultSettings->[0]->{removeTrailingWhitespace};
+my $cycleThroughBackUps = $defaultSettings->[0]->{cycleThroughBackUps};
 
 # hash variables
 my %lookForAlignDelims= %{$defaultSettings->[0]->{lookForAlignDelims}};
@@ -206,6 +225,9 @@ my %checkunmatchedELSE= %{$defaultSettings->[0]->{checkunmatchedELSE}};
 my %checkunmatchedbracket= %{$defaultSettings->[0]->{checkunmatchedbracket}};
 my %noAdditionalIndent= %{$defaultSettings->[0]->{noAdditionalIndent}};
 my %indentAfterHeadings= %{$defaultSettings->[0]->{indentAfterHeadings}};
+my %indentAfterItems= %{$defaultSettings->[0]->{indentAfterItems}};
+my %itemNames= %{$defaultSettings->[0]->{itemNames}};
+my %constructIfElseFi= %{$defaultSettings->[0]->{constructIfElseFi}};
 
 # need new hashes to store the user and local data before
 # overwriting the default
@@ -218,6 +240,9 @@ my %checkunmatchedELSEUSER;
 my %checkunmatchedbracketUSER;
 my %noAdditionalIndentUSER;
 my %indentAfterHeadingsUSER;
+my %indentAfterItemsUSER;
+my %itemNamesUSER;
+my %constructIfElseFiUSER;
 
 # for printing the user and local settings to the log file
 my %dataDump;
@@ -230,7 +255,7 @@ my $userSettings;
 
 # get information about user settings- first check if indentconfig.yaml exists
 my $indentconfig = File::HomeDir->my_home . "/indentconfig.yaml";
-if ( -e $indentconfig and !$onlyDefault ) 
+if ( -e $indentconfig and !$onlyDefault )
 {
       print $logfile "Reading path information from ",File::HomeDir->my_home,"/indentconfig.yaml\n";
 
@@ -248,13 +273,13 @@ if ( -e $indentconfig and !$onlyDefault )
       else
       {
         print $logfile <<ENDQUOTE
-WARNING:  $indentconfig 
+WARNING:  $indentconfig
           contains some invalid .yaml formatting- unable to read from it.
-          No user settings loaded. 
+          No user settings loaded.
 ENDQUOTE
 ;
       }
-} 
+}
 else
 {
       if($onlyDefault)
@@ -275,16 +300,16 @@ else
 my $directoryName = dirname $ARGV[0];
 
 # add local settings to the paths, if appropriate
-if ( (-e "$directoryName/localSettings.yaml") and $readLocalSettings and !(-z "$directoryName/localSettings.yaml")) 
+if ( (-e "$directoryName/localSettings.yaml") and $readLocalSettings and !(-z "$directoryName/localSettings.yaml"))
 {
-    print $logfile "\nAdding ./localSettings.yaml to paths\n\n";
+    print $logfile "\nAdding $directoryName/localSettings.yaml to paths\n\n";
     push(@absPaths,"$directoryName/localSettings.yaml");
 }
-elsif ( !(-e "$directoryName/localSettings.yaml") and $readLocalSettings) 
+elsif ( !(-e "$directoryName/localSettings.yaml") and $readLocalSettings)
 {
       print $logfile "WARNING\n\t$directoryName/localSettings.yaml not found\n";
       print $logfile "\tcarrying on without it.\n";
-} 
+}
 
 # read in the settings from each file
 foreach my $settings (@absPaths)
@@ -312,8 +337,9 @@ foreach my $settings (@absPaths)
             $onlyOneBackUp = $userSettings->[0]->{onlyOneBackUp} if defined($userSettings->[0]->{onlyOneBackUp});
             $maxNumberOfBackUps = $userSettings->[0]->{maxNumberOfBackUps} if defined($userSettings->[0]->{maxNumberOfBackUps});
             $removeTrailingWhitespace = $userSettings->[0]->{removeTrailingWhitespace} if defined($userSettings->[0]->{removeTrailingWhitespace});
+            $cycleThroughBackUps = $userSettings->[0]->{cycleThroughBackUps} if defined($userSettings->[0]->{cycleThroughBackUps});
 
-            # hash variables - note that each one requires two lines, 
+            # hash variables - note that each one requires two lines,
             # one to read in the data, one to put the keys&values in correctly
 
             %lookForAlignDelimsUSER= %{$userSettings->[0]->{lookForAlignDelims}} if defined($userSettings->[0]->{lookForAlignDelims});
@@ -340,6 +366,14 @@ foreach my $settings (@absPaths)
             %indentAfterHeadingsUSER= %{$userSettings->[0]->{indentAfterHeadings}} if defined($userSettings->[0]->{indentAfterHeadings});
             @indentAfterHeadings{ keys %indentAfterHeadingsUSER } = values %indentAfterHeadingsUSER if (%indentAfterHeadingsUSER);
 
+            %indentAfterItemsUSER= %{$userSettings->[0]->{indentAfterItems}} if defined($userSettings->[0]->{indentAfterItems});
+            @indentAfterItems{ keys %indentAfterItemsUSER } = values %indentAfterItemsUSER if (%indentAfterItemsUSER);
+
+            %itemNamesUSER= %{$userSettings->[0]->{itemNames}} if defined($userSettings->[0]->{itemNames});
+            @itemNames{ keys %itemNamesUSER } = values %itemNamesUSER if (%itemNamesUSER);
+
+            %constructIfElseFiUSER= %{$userSettings->[0]->{constructIfElseFi}} if defined($userSettings->[0]->{constructIfElseFi});
+            @constructIfElseFi{ keys %constructIfElseFiUSER } = values %constructIfElseFiUSER if (%constructIfElseFiUSER);
        }
        else
        {
@@ -371,13 +405,14 @@ if ($overwrite)
     print $logfile "\nBackup procedure:\n";
     # original name of file
     my $filename = $ARGV[0];
-    # copy it
-    my $backupFile = $filename;
+
+    # get the base file name, allowing for different extensions
+    my $backupFile = basename($filename,(".tex",".sty",".cls"));
 
     # add the user's backup directory to the backup path
     $backupFile = "$cruftDirectory/$backupFile";
 
-    # if both ($onlyOneBackUp and $maxNumberOfBackUps) then we have 
+    # if both ($onlyOneBackUp and $maxNumberOfBackUps) then we have
     # a conflict- er on the side of caution and turn off onlyOneBackUp
     if($onlyOneBackUp and $maxNumberOfBackUps>1)
     {
@@ -386,7 +421,7 @@ if ($overwrite)
         $onlyOneBackUp = 0;
     }
 
-    # if the user has specified that $maxNumberOfBackUps = 1 then 
+    # if the user has specified that $maxNumberOfBackUps = 1 then
     # they only want one backup
     if($maxNumberOfBackUps==1)
     {
@@ -407,7 +442,7 @@ if ($overwrite)
     # be overwritten each time
     if($onlyOneBackUp)
     {
-        $backupFile =~ s/\.tex/$backupExtension/;
+        $backupFile .= $backupExtension;
         print $logfile "\t copying $filename to $backupFile\n";
         print $logfile "\t $backupFile was overwritten\n\n" if (-e $backupFile);
     }
@@ -415,7 +450,7 @@ if ($overwrite)
     {
         # start with a backup file .bak0 (or whatever $backupExtension is present)
         my $backupCounter = 0;
-        $backupFile =~ s/\.tex$/$backupExtension$backupCounter/;
+        $backupFile .= $backupExtension.$backupCounter;
 
         # if it exists, then keep going: .bak0, .bak1, ...
         while (-e $backupFile or $maxNumberOfBackUps>1)
@@ -423,6 +458,36 @@ if ($overwrite)
             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
                 $maxNumberOfBackUps=1 ;
                 last; # break out of the loop
             }
@@ -444,7 +509,7 @@ if ($overwrite)
     copy($filename,$backupFile) or die "Could not write to backup file $backupFile. Please check permissions. Exiting.\n";
 }
 
-if(!($outputToFile or $overwrite)) 
+if(!($outputToFile or $overwrite))
 {
     print $logfile "Just out put to the terminal :)\n\n" if !$silentMode  ;
 }
@@ -460,28 +525,28 @@ my $inverbatim=0;           # $inverbatim: switch to determine if in
 my $delimiters=0;           # $delimiters: switch that governs if
                             #              we need to check for & or not
 my $matchedbraces=0;        # $matchedbraces: counter to see if { }
-                            #               are matched; it will be 
-                            #               positive if too many { 
+                            #               are matched; it will be
+                            #               positive if too many {
                             #               negative if too many }
                             #               0 if matched
 my $matchedBRACKETS=0;      # $matchedBRACKETS: counter to see if [ ]
-                            #               are matched; it will be 
-                            #               positive if too many { 
+                            #               are matched; it will be
+                            #               positive if too many {
                             #               negative if too many }
                             #               0 if matched
 my $commandname;            # $commandname: either \parbox, \marginpar,
                             #               or anything else from %checkunmatched
 my $commanddetails;         # $command details: a scalar that stores
-                            #               details about the command 
+                            #               details about the command
                             #               that splits {} across lines
-my $countzeros;             # $countzeros:  a counter that helps 
+my $countzeros;             # $countzeros:  a counter that helps
                             #               when determining if we're in
                             #               an else construct
-my $lookforelse=0;          # $lookforelse: a boolean to help determine 
-                            #               if we need to look for an 
+my $lookforelse=0;          # $lookforelse: a boolean to help determine
+                            #               if we need to look for an
                             #               else construct
-my $trailingcomments;       # $trailingcomments stores the comments at the end of 
-                            #           a line 
+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
@@ -492,26 +557,26 @@ my $headingLevel=0;         # $headingLevel: scalar that stores which heading
 my @indent;                 # @indent: stores current level of indentation
 my @lines;                  # @lines: stores the newly indented lines
 my @block;                  # @block: stores blocks that have & delimiters
-my @commandstore;           # @commandstore: stores commands that 
+my @commandstore;           # @commandstore: stores commands that
                             #           have split {} across lines
-my @commandstorebrackets;   # @commandstorebrackets: stores commands that 
+my @commandstorebrackets;   # @commandstorebrackets: stores commands that
                             #           have split [] across lines
-my @mainfile;               # @mainfile: stores input file; used to 
+my @mainfile;               # @mainfile: stores input file; used to
                             #            grep for \documentclass
 my @headingStore;           # @headingStore: stores headings: chapter, section, etc
-my @indentNames;            # @indentNames: keeps names of commands and 
+my @indentNames;            # @indentNames: keeps names of commands and
                             #               environments that have caused
                             #               indentation to increase
-my @environmentStack;       # @environmentStack: stores the (nested) names 
+my @environmentStack;       # @environmentStack: stores the (nested) names
                             #                    of environments
 
-# check to see if the current file has \documentclass, if so, then 
+# 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, $ARGV[0]) or die "Could not open input file";
     @mainfile=<MAINFILE>;
 close(MAINFILE);
 
-# if the MAINFILE doesn't have a \documentclass statement, then 
+# if the MAINFILE doesn't have a \documentclass statement, then
 # it shouldn't have preamble
 if(scalar(@{[grep(m/^\s*\\documentclass/, @mainfile)]})==0)
 {
@@ -532,7 +597,7 @@ while(<MAINFILE>)
 {
     # increment the line counter
     $lineCounter++;
-    
+
     # tracing mode
     print $logfile "\n" if($tracingMode and !($inpreamble or $inverbatim or $inIndentBlock));
 
@@ -542,10 +607,10 @@ while(<MAINFILE>)
     {
         # if not, remove all leading spaces and tabs
         # from the current line, assuming it isn't empty
-        #s/^\ *//; 
-        #s/^\s+//; 
-        #s/^\t+//; 
-        s/^\t*// if($_ !~ /^((\s*)|(\t*))*$/); 
+        #s/^\ *//;
+        #s/^\s+//;
+        #s/^\t+//;
+        s/^\t*// if($_ !~ /^((\s*)|(\t*))*$/);
         s/^\s*// if($_ !~ /^((\s*)|(\t*))*$/);
 
         # tracing mode
@@ -580,19 +645,28 @@ while(<MAINFILE>)
         }
     }
 
+    # \END{ENVIRONMENTS}, or CLOSING } or CLOSING ]
+    # \END{ENVIRONMENTS}, or CLOSING } or CLOSING ]
+    # \END{ENVIRONMENTS}, or CLOSING } or CLOSING ]
+
+    print $logfile "Line $lineCounter\t << PHASE 1: looking for reasons to DECREASE indentation of CURRENT line \n" if($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're at the end of a noindent 
+    # 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
-    if(!($inverbatim or $inpreamble or $inIndentBlock))
+    # noIndentBlock or in a delimiter block
+    if(!($inverbatim or $inpreamble or $inIndentBlock or $delimiters))
     {
-        # The check for closing } and ] relies on counting, so 
+        # 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
         #
@@ -615,13 +689,19 @@ while(<MAINFILE>)
         # 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 
+        # 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
+        # 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))
         {
@@ -630,21 +710,23 @@ while(<MAINFILE>)
             $_ = $_ . $trailingcomments."\n" ;
 
             # tracing mode
-            print $logfile "Line $lineCounter\t counting braces/brackets complete: added trailing comments back on $trailingcomments\n" if($tracingMode);
+            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/;
+        }
     }
 
-    # remove trailing whitespace
-    if ($removeTrailingWhitespace)
-    {
-        print $logfile "Line $lineCounter\t removing trailing whitespace\n" if ($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)
@@ -666,7 +748,7 @@ while(<MAINFILE>)
             }
             push(@lines,$_);
             # tracing mode
-            print $logfile "Line $lineCounter\t Adding current level of indentation: ",join(", ",@indentNames),"\n" if($tracingMode);
+            print $logfile "Line $lineCounter\t || PHASE 2: Adding current level of indentation: ",join(", ",@indentNames),"\n" if($tracingMode);
         }
     }
     else
@@ -678,21 +760,39 @@ while(<MAINFILE>)
         print $logfile "Line $lineCounter\t In delimeter block, waiting for block formatting\n" if($tracingMode);
     }
 
-    # only check for new environments or commands if we're 
+    # \BEGIN{ENVIRONMENT} or OPEN { or OPEN [
+    # \BEGIN{ENVIRONMENT} or OPEN { or OPEN [
+    # \BEGIN{ENVIRONMENT} or OPEN { or OPEN [
+
+    # 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))
     {
 
-        # check if we are in a 
+        print $logfile "Line $lineCounter\t >> PHASE 3: looking for reasons to INCREASE indentation of SUBSEQUENT lines \n" if($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 
+        # 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();
+
         # remove trailing comments so that any {, }, [, ]
         # that are found after % are not counted
         #
@@ -706,7 +806,7 @@ while(<MAINFILE>)
         # 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 \[ 
+        # check to see if we have \begin{something} or \[
         &at_beg_of_env_or_eq();
 
         # check to see if we have \parbox, \marginpar, or
@@ -714,7 +814,7 @@ while(<MAINFILE>)
         # specified in %checkunmatched hash table
         &start_command_or_key_unmatched_braces();
 
-        # check for an else statement
+        # check for an else statement (braces, not \else)
         &check_for_else();
 
         # check for a command that splits [] across lines
@@ -723,6 +823,12 @@ while(<MAINFILE>)
         # check for a heading
         &indent_after_heading();
 
+        # check for \item
+        &indent_after_item();
+
+        # check for \if or \else command
+        &indent_after_if_else_fi();
+
         # tracing mode
         print $logfile "Line $lineCounter\t Environments: ",join(", ",@environmentStack),"\n" if($tracingMode and scalar(@environmentStack));
     }
@@ -737,7 +843,7 @@ print $logfile "Line Count of indented $ARGV[0]: ",scalar(@lines);
 if(scalar(@mainfile) != scalar(@lines))
 {
   print $logfile <<ENDQUOTE
-WARNING: \t line count of original file and indented file does 
+WARNING: \t line count of original file and indented file does
 \t not match- consider reverting to a back up, see $backupExtension;
 ENDQUOTE
 ;
@@ -771,6 +877,162 @@ close($logfile);
 
 exit;
 
+sub indent_if_else_fi{
+    # PURPOSE: set indentation of line that contains \else, \fi  command
+    #
+    #
+
+    # @indentNames could be empty -- if so, exit
+    return 0 unless(@indentNames);
+
+    # look for \fi
+    if( $_ =~ m/^\s*\\fi/ and $constructIfElseFi{$indentNames[-1]})
+    {
+        # tracing mode
+        print $logfile "Line $lineCounter\t \\fi command found, matching: \\",$indentNames[-1], "\n" if($tracingMode);
+        &decrease_indent($indentNames[-1]);
+    }
+    elsif( ($_ =~ m/^\s*\\else/ or $_ =~ m/^\s*\\or/) and $constructIfElseFi{$indentNames[-1]})
+    {
+        # tracing mode
+        print $logfile "Line $lineCounter\t \\else command found, matching: \\",$indentNames[-1], "\n" if($tracingMode);
+        print $logfile "Line $lineCounter\t decreasing indent, but indentNames is still  \\",join(", ",@indentNames), "\n" if($tracingMode);
+        pop(@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 #
+    if( $_ =~ m/^\s*\\(if.*?)(\s|\\|\#)/ and $constructIfElseFi{$1})
+    {
+        # tracing mode
+        print $logfile "Line $lineCounter\t ifelsefi construct found: $1 \n" if($tracingMode);
+        &increase_indent($1);
+    }
+    elsif(@indentNames)
+    {
+        if( ($_ =~ m/^\s*\\else/ or $_ =~ m/^\s*\\or/ ) and $constructIfElseFi{$indentNames[-1]})
+        {
+            # tracing mode
+            print $logfile "Line $lineCounter\t setting indent *after* \\else or \\or command found for $indentNames[-1] \n" if($tracingMode);
+            &increase_indent($indentNames[-1]);
+            # don't want to store the name of the \if construct twice
+            # so remove the second copy
+            pop(@indentNames);
+        }
+  }
+  }
+
+sub indent_item{
+    # PURPOSE: this subroutine sets the indentation for the item *itself*
+
+    if( $_ =~ m/^\s*\\(.*?)(\[|\s)/ and $itemNames{$1} and $indentAfterItems{$environmentStack[-1]})
+    {
+        # tracing mode
+        print $logfile "Line $lineCounter\t $1 found within ",$environmentStack[-1]," environment (see indentAfterItems and itemNames)\n" if($tracingMode);
+        if($itemNames{$indentNames[-1]})
+        {
+            print $logfile "Line $lineCounter\t $1 found- neutralizing indentation from previous ",$indentNames[-1],"\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
+    #
+    if( $_ =~ m/^\s*\\(.*?)(\[|\s)/
+            and $itemNames{$1}
+            and $indentAfterItems{$environmentStack[-1]})
+    {
+        # tracing mode
+        print $logfile "Line $lineCounter\t $1 found within ",$environmentStack[-1]," environment (see indentAfterItems and itemNames)\n" if($tracingMode);
+        &increase_indent($1);
+    }
+}
+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})
+    {
+           $delimiters=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}
+    #                     }
+
+    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();
+        }
+        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
@@ -783,7 +1045,7 @@ sub indent_heading{
     #
     #           and anything else listed in indentAfterHeadings
     #
-    #           This subroutine specifies the indentation for the 
+    #           This subroutine specifies the indentation for the
     #           heading itself, i.e the line that has \chapter, \section etc
     if( $_ =~ m/^\s*\\(.*?)(\[|{)/ and $indentAfterHeadings{$1})
     {
@@ -796,15 +1058,15 @@ sub indent_heading{
        # local scalar
        my $previousHeadingLevel = $headingLevel;
 
-       # if current heading level < old heading level, 
+       # 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 
+            # 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))  
+
+            if(scalar(@headingStore))
             {
                while($currentHeading{level}<$previousHeadingLevel and scalar(@headingStore))
                {
@@ -823,7 +1085,7 @@ sub indent_heading{
        }
        elsif($currentHeading{level}==$previousHeadingLevel)
        {
-            if(scalar(@headingStore))  
+            if(scalar(@headingStore))
             {
                  my $higherHeadingName = pop(@headingStore);
                  my %higherLevelHeading = %{$indentAfterHeadings{$higherHeadingName}};
@@ -852,7 +1114,7 @@ sub indent_after_heading{
     #
     #           and anything else listed in indentAfterHeadings
     #
-    #           This subroutine is specifies the indentation for 
+    #           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})
@@ -880,7 +1142,7 @@ sub at_end_noindent{
     #          This is for blocks of code that the user wants
     #          to leave untouched- similar to verbatim blocks
 
-    if( $_ =~ m/^%\s*\\end{(.*?)}/ and $noIndentBlock{$1}) 
+    if( $_ =~ m/^%\s*\\end{(.*?)}/ and $noIndentBlock{$1})
     {
             $inIndentBlock=0;
             # tracing mode
@@ -888,6 +1150,8 @@ sub at_end_noindent{
     }
 }
 
+
+
 sub at_beg_noindent{
     # PURPOSE: This matches
     #           % \begin{noindent}
@@ -899,7 +1163,7 @@ sub at_beg_noindent{
     #          This is for blocks of code that the user wants
     #          to leave untouched- similar to verbatim blocks
 
-    if( $_ =~ m/^%\s*\\begin{(.*?)}/ and $noIndentBlock{$1}) 
+    if( $_ =~ m/^%\s*\\begin{(.*?)}/ and $noIndentBlock{$1})
     {
            $inIndentBlock = 1;
            # tracing mode
@@ -908,11 +1172,11 @@ sub at_beg_noindent{
 }
 
 sub start_command_or_key_unmatched_brackets{
-    # PURPOSE: This matches 
+    # PURPOSE: This matches
     #              \pgfplotstablecreatecol[...
     #
-    #              or any other command/key that has brackets [ ] 
-    #              split across lines specified in the 
+    #              or any other command/key that has brackets [ ]
+    #              split across lines specified in the
     #              hash tables, %checkunmatchedbracket
     #
     # How to read: ^\s*(\\)?(.*?)(\[\s*)
@@ -924,7 +1188,7 @@ sub start_command_or_key_unmatched_brackets{
     #       ((?<!\\)\[\s*) match [ possibly leading with spaces
     #                      but it WON'T match \[
 
-    if ($_ =~ m/^\s*(\\)?(.*?)(\s*(?<!\\)\[)/ 
+    if ($_ =~ m/^\s*(\\)?(.*?)(\s*(?<!\\)\[)/
         and (scalar($checkunmatchedbracket{$2})
              or $alwaysLookforSplitBrackets)
         )
@@ -957,13 +1221,13 @@ sub start_command_or_key_unmatched_brackets{
 }
 
 sub end_command_or_key_unmatched_brackets{
-    # PURPOSE:  Check for the closing BRACKET of a command that 
+    # 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 @commandstorebrackets, and making 
+    #           in the array @commandstorebrackets, and making
     #           sure that we're not starting another command/key
     #           that has split BRACKETS (nesting).
     #
@@ -971,8 +1235,8 @@ sub end_command_or_key_unmatched_brackets{
     #
     #           We count the number of [ and ADD to the counter
     #                                  ] and SUBTRACT to the counter
-    if(scalar(@commandstorebrackets) 
-        and  !($_ =~ m/^\s*(\\)?(.*?)(\s*\[)/ 
+    if(scalar(@commandstorebrackets)
+        and  !($_ =~ m/^\s*(\\)?(.*?)(\s*\[)/
                     and (scalar($checkunmatchedbracket{$2})
                          or $alwaysLookforSplitBrackets))
         and $_ !~ m/^\s*%/
@@ -1013,7 +1277,7 @@ sub end_command_or_key_unmatched_brackets{
 }
 
 sub start_command_or_key_unmatched_braces{
-    # PURPOSE: This matches 
+    # PURPOSE: This matches
     #              \parbox{...
     #              \parbox[..]..{
     #              empty header/.style={
@@ -1021,7 +1285,7 @@ sub start_command_or_key_unmatched_braces{
     #              etc
     #
     #              or any other command/key that has BRACES
-    #              split across lines specified in the 
+    #              split across lines specified in the
     #              hash tables, %checkunmatched, %checkunmatchedELSE
     #
     # How to read: ^\s*(\\)?(.*?)(\[|{|\s)
@@ -1032,8 +1296,8 @@ sub start_command_or_key_unmatched_braces{
     #       (.*?)              non-greedy character match and store the result
     #       (\[|}|=|(\s*\\))   either [ or { or = or space \
 
-    if ($_ =~ m/^\s*(\\)?(.*?)(\[|{|=|(\s*\\))/ 
-            and (scalar($checkunmatched{$2}) 
+    if ($_ =~ m/^\s*(\\)?(.*?)(\[|{|=|(\s*\\))/
+            and (scalar($checkunmatched{$2})
                  or scalar($checkunmatchedELSE{$2})
                  or $alwaysLookforSplitBraces)
         )
@@ -1079,7 +1343,7 @@ sub start_command_or_key_unmatched_braces{
             {
                 # 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)
                 {
@@ -1087,6 +1351,9 @@ sub start_command_or_key_unmatched_braces{
                      # store the match, either { or }
                      my $braceType = $1;
 
+                     # exit the loop if @commandstore is empty
+                     last if(!@commandstore);
+
                      # get the details of the most recent command name
                      $commanddetails = pop(@commandstore);
                      $commandname = $commanddetails->{'commandname'};
@@ -1119,7 +1386,7 @@ sub start_command_or_key_unmatched_braces{
                      }
                      else
                      {
-                            # otherwise we need to put the command back for the 
+                            # otherwise we need to put the command back for the
                             # next brace count
                             push(@commandstore,{commandname=>$commandname,
                                                 matchedbraces=>$matchedbraces,
@@ -1132,17 +1399,17 @@ sub start_command_or_key_unmatched_braces{
 }
 
 sub end_command_or_key_unmatched_braces{
-    # PURPOSE:  Check for the closing BRACE of a command that 
+    # 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 @commandstore, and making 
+    #           in the array @commandstore, and making
     #           sure that we're not starting another command/key
     #           that has split BRACES (nesting).
     #
@@ -1150,9 +1417,9 @@ sub end_command_or_key_unmatched_braces{
     #
     #           We count the number of { and ADD to the counter
     #                                  } and SUBTRACT to the counter
-    if(scalar(@commandstore) 
-      and  !($_ =~ m/^\s*(\\)?(.*?)(\[|{|=|(\s*\\))/ 
-                    and (scalar($checkunmatched{$2}) 
+    if(scalar(@commandstore)
+      and  !($_ =~ m/^\s*(\\)?(.*?)(\[|{|=|(\s*\\))/
+                    and (scalar($checkunmatched{$2})
                          or scalar($checkunmatchedELSE{$2})
                          or $alwaysLookforSplitBraces))
         and $_ !~ m/^\s*%/
@@ -1164,6 +1431,9 @@ sub end_command_or_key_unmatched_braces{
             # store the match, either { or }
             my $braceType = $1;
 
+            # exit the loop if @commandstore is empty
+            last if(!@commandstore);
+
             # get the details of the most recent command name
             $commanddetails = pop(@commandstore);
             $commandname = $commanddetails->{'commandname'};
@@ -1223,17 +1493,17 @@ sub check_for_else{
     #                   else this
     #               }
     #
-    #          so we need to look for the else bit, and set 
+    #          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 @commandstore, and if 
-    #          the line itself is not a command, or comment, 
+    #          in the array @commandstore, and if
+    #          the line itself is not a command, or comment,
     #          and if it begins with {
 
-    if(scalar(@commandstore) 
-        and  !($_ =~ m/^\s*(\\)?(.*?)(\[|{|=)/ 
-                    and (scalar($checkunmatched{$2}) 
+    if(scalar(@commandstore)
+        and  !($_ =~ m/^\s*(\\)?(.*?)(\[|{|=)/
+                    and (scalar($checkunmatched{$2})
                          or scalar($checkunmatchedELSE{$2})
                          or $alwaysLookforSplitBraces))
         and $_ =~ m/^\s*{/
@@ -1272,11 +1542,11 @@ sub at_beg_of_env_or_eq{
     #               \[
     #
     #          It also checks to see if the current environment
-    #          should have alignment delimiters; if so, we need to turn 
-    #          ON the $delimiter switch 
+    #          should have alignment delimiters; if so, we need to turn
+    #          ON the $delimiter switch
 
     # How to read
-    #  m/^\s*(\$)?\\begin{(.*?)}/ 
+    #  m/^\s*(\$)?\\begin{(.*?)}/
     #
     #   ^               beginning of a line
     #   \s*             any white spaces (possibly none)
@@ -1289,16 +1559,19 @@ sub at_beg_of_env_or_eq{
     #  ^        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 
+    #  (\\\[)   \[  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}/) 
+    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 the indentation
        &increase_indent($2);
 
        # check for verbatim-like environments
@@ -1345,12 +1618,14 @@ sub at_end_of_env_or_eq{
     #          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 $delimiter switch 
-    
-    if( ($_ =~ m/^\s*\\end{(.*?)}/ or $_=~ m/^(\\\])/)
-         and $_ !~ m/\s*^%/)
+    #          had alignment delimiters; if so, we need to turn
+    #          OFF the $delimiter switch
+
+    if( ($_ =~ m/^\s*\\end{\\?(.*?)}/ or $_=~ m/^(\\\])/) and $_ !~ m/\s*^%/)
     {
 
        # check if we're at the end of a verbatim-like environment
@@ -1361,79 +1636,110 @@ sub at_end_of_env_or_eq{
 
             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 ""); 
+            #s/^\ *//;
+            s/^\t+// if($_ ne "");
+            s/^\s+// if($_ ne "");
        }
 
-       # check to see if \end{environment} fits with most recent \begin{...}
-       my $previousEnvironment = pop(@environmentStack);
-
-       # check to see if we need to turn off alignment
-       # delimiters and output the current block
-       if($lookForAlignDelims{$1} and ($previousEnvironment eq $1))
+       # check if we're in an environment that is looking
+       # to indent after each \item
+       if(scalar(@indentNames) and $itemNames{$indentNames[-1]})
        {
-           $delimiters=0;
+            &decrease_indent($indentNames[-1]);
+       }
 
-           # tracing mode
-           print $logfile "Line $lineCounter\t Delimiter body FINISHED: $1\n" if($tracingMode);
+       # some commands contain \end{environmentname}, which 
+       # can cause a problem if \begin{environmentname} was not 
+       # started previously; if @environmentStack is empty, 
+       # then we don't need to check for \end{environmentname}
+       if(@environmentStack)
+       {
+          # check to see if \end{environment} fits with most recent \begin{...}
+          my $previousEnvironment = pop(@environmentStack);
 
-           # print the current FORMATTED block
-           @block = &format_block(@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)
-                {
-                    $line = join("",@indent).$line;
-                }
-                push(@lines,$line);
-           }
-           # empty the @block, very important!
-           @block=();
-       }
+          # check to see if we need to turn off alignment
+          # delimiters and output the current block
+          if($lookForAlignDelims{$1} and ($previousEnvironment eq $1))
+          {
+               &print_aligned_block();
+          }
 
-       # tracing mode
-       print $logfile "Line $lineCounter\t \\end{envrionment} found: $1 \n" if($tracingMode and !$verbatimEnvironments{$1});
+          # tracing mode
+          print $logfile "Line $lineCounter\t \\end{envrionment} found: $1 \n" if($tracingMode and !$verbatimEnvironments{$1});
 
-       # check to see if \end{environment} fits with most recent \begin{...}
-       if($previousEnvironment eq $1)
-       {
-            # decrease the indentation (if appropriate)
-            &decrease_indent($1);
-       }
-       else
-       {
-           # otherwise put the environment name back on the stack
-           push(@environmentStack,$previousEnvironment);
-           print $logfile "Line $lineCounter\t WARNING: \\end{$1} found on its own line, not matched to \\begin{$previousEnvironment}\n" unless ($delimiters or $inverbatim or $inIndentBlock or $1 eq "\\\]");
-       }
+          # check to see if \end{environment} fits with most recent \begin{...}
+          if($previousEnvironment eq $1)
+          {
+               # decrease the indentation (if appropriate)
+               &decrease_indent($1);
+          }
+          else
+          {
+              # otherwise put the environment name back on the stack
+              push(@environmentStack,$previousEnvironment);
+              print $logfile "Line $lineCounter\t WARNING: \\end{$1} found on its own line, not matched to \\begin{$previousEnvironment}\n" unless ($delimiters or $inverbatim or $inIndentBlock or $1 eq "\\\]");
+          }
 
-       # need a special check for \[ and \]
-       if($1 eq "\\\]")
-       {
-            &decrease_indent($1);
-            pop(@environmentStack);
+          # need a special check for \[ and \]
+          if($1 eq "\\\]")
+          {
+               &decrease_indent($1);
+               pop(@environmentStack);
+          }
        }
 
-       # if we're at the end of the document, we remove all current 
-       # indentation- this is especially prominent in examples that 
+       # 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($1 eq "document" and !(grep(/filecontents/, @indentNames)) and !$inpreamble and !$delimiters and !$inverbatim and !$inIndentBlock)
        {
-            @indent=(); 
-            @indentNames=(); 
-            print $logfile "Line $lineCounter\t \\end{$1} found- emptying indent array \n" unless ($delimiters or $inverbatim or $inIndentBlock or $1 eq "\\\]");
+            @indent=();
+            @indentNames=();
+
+            # tracing mode
+            if($tracingMode)
+            {
+                print $logfile "Line $lineCounter\t \\end{$1} found- emptying indent array \n" unless ($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: $1\n" if($tracingMode);
+
+    # print the current FORMATTED block
+    @block = &format_block(@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)
+         {
+             $line = join("",@indent).$line;
+         }
+         push(@lines,$line);
+    }
+    # empty the @block, very important!
+    @block=();
+}
+
 sub format_block{
-    #   PURPOSE: Format a delimited environment such as the 
+    #   PURPOSE: Format a delimited environment such as the
     #            tabular or align environment that contains &
     #
     #   INPUT: @block               array containing unformatted block
@@ -1448,7 +1754,7 @@ sub format_block{
     print $logfile "\t\tFormatting alignment block\n" if($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 
+    # it will be increased back to the end of the block in the
     # loop later on:  foreach $row (@tmpblock)
     $lineCounter -= scalar(@block);
 
@@ -1479,7 +1785,7 @@ sub format_block{
     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 
+    # 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)
     {
@@ -1512,7 +1818,7 @@ sub format_block{
 
     # 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)
     {
@@ -1560,11 +1866,11 @@ sub format_block{
             {
                # 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)
@@ -1583,7 +1889,7 @@ sub format_block{
                }
             }
 
-            
+
             # put $linebreak back on the string, now that
             # the measurement has been done
             $tmpstring .= $linebreak;
@@ -1598,7 +1904,7 @@ sub format_block{
         }
         else
         {
-               # if there are no & then use the 
+               # if there are no & then use the
                # NOFORMATTING token
                # remove leading space
     	       s/^\s+//;
@@ -1632,16 +1938,16 @@ sub format_block{
     #       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 $row (@tmpblock)
     {
@@ -1689,7 +1995,7 @@ sub format_block{
         # remove trailing whitespace
         if ($removeTrailingWhitespace)
         {
-            print $logfile "Line $lineCounter\t removing trailing whitespace from delimiter aligned line\n" if ($tracingMode);
+            print $logfile "\t\tLine $lineCounter\t removing trailing whitespace from delimiter aligned line\n" if ($tracingMode);
             $tmpstring =~ s/\s+$/\n/;
         }
 
@@ -1711,7 +2017,7 @@ sub increase_indent{
 
        my $command = pop(@_);
 
-       # if the user has specified $indentRules{$command} and 
+       # 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}
@@ -1726,7 +2032,7 @@ sub increase_indent{
             delete $indentRules{$command};
        }
 
-       # if the command is in verbatimEnvironments and in indentRules then 
+       # 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})
@@ -1745,7 +2051,7 @@ sub increase_indent{
           push(@indent, $indentRules{$command});
           # tracing mode
           print $logfile "Line $lineCounter\t increasing indent using rule for $command (see indentRules)\n" if($tracingMode);
-          push(@indentNames,"$command (rule)");
+          push(@indentNames,"$command");
        }
        else
        {
@@ -1753,7 +2059,7 @@ sub increase_indent{
           if(!($noAdditionalIndent{$command} or $verbatimEnvironments{$command} or $inverbatim))
           {
             push(@indent, $defaultIndent);
-            push(@indentNames,"$command (default)");
+            push(@indentNames,"$command");
             # tracing mode
             print $logfile "Line $lineCounter\t increasing indent using defaultIndent\n" if($tracingMode);
           }
@@ -1775,10 +2081,21 @@ sub decrease_indent{
 
        if(!($noAdditionalIndent{$command} or $verbatimEnvironments{$command} or $inverbatim))
        {
+            print $logfile "Line $lineCounter\t removing ", $indentNames[-1], " from indentNames\n" if($tracingMode);
             pop(@indent);
             pop(@indentNames);
             # tracing mode
-            print $logfile "Line $lineCounter\t decreasing indent to: ",join(", ",@indentNames),"\n" if($tracingMode);
+            if($tracingMode)
+            {
+                if(@indentNames)
+                {
+                    print $logfile "Line $lineCounter\t decreasing indent to: ",join(", ",@indentNames),"\n" ;
+                }
+                else
+                {
+                    print $logfile "Line $lineCounter\t indent now empty \n";
+              }
+            }
        }
 }