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THE PROBLEM
-----------
In parser.php, this is generated by default:
   <span class="tocnumber">1</span> ...
We want this
   <span class="tocnumber">1.</span> ...

So we don't have headings like these that appear to give a 
content-count that isn't intended:
  1 Overview
  2 Major Enhancements
  3 Significant Changes
  4 Bugs Fixed
  5 Open Issues

We want this instead, especially when using the __NUMBEREDHEADINGS__ 
extension, so the headings don't mislead readers:
  1. Overview
  2. Major Enhancements
  3. Significant Changes
  4. Bugs Fixed
  5. Open Issues

MY PATCH
--------
In includes/parser/parser.php, I replaced replaced lines 3509..3520
(from comment at the top of the section to the end of the for loop),
with these lines:
                # count number of headlines for each level
                @$sublevelCount[$toclevel]++;    
                    # An array of heading numbers, one per level, where everything
                    #   after 1.2 (for example) is "empty": [1, 2, empty, empty, empty]
                $dot = 0;    # No dot before the first number.
                for( $i = 1; $i <= $toclevel; $i++ ) {
                    if( !empty( $sublevelCount[$i] ) ) {
                        // Add a dot before this non-empty sublevel index
                        // (There's no dot after the last one)
                        if( $dot ) {                    
                            $numbering .= '.';
                        }
                        $numbering .= $wgContLang->formatNum( $sublevelCount[$i] );
                        $dot = 1;
                    }
                }
                if ($toclevel == 1) {
                    # We're at a level one head. Add a dot after it.   
                    $numbering .= '.';
                }
                }