Renumbers footnotes in a markdown file in sequential order

fnprocess.php

<?php

// This renumbers footnotes in a markdown file in the order they appear, both in the text and citations
// Insert new footnotes in the order in which they should appear, in both text and citation
// Use a unique identifier for each new footnote ie [^fn1a], [^fn2a], etc.
// Place your footnotes at the end of the file with your full text.
// Separate them from the main text with the header `# Footnotes`
//
// This is meant to be run from the command line
// Run "php fnprocess.php -fFILENAME.MD" where FILENAME.MD is the name of the input file
// If you'd rather not specify a filename, this looks for "input.md" by default
// Original text with renumbered footnotes will be saved in "output.md"


 function updateFootnotes($text){

    $regex = '/fn\d{1,3}/';
    preg_match_all($regex, $text, $matches);
    $total = count($matches[0]);
  
    // Uncomment the following two lines if you want verbose output
    // echo ("<h2>".count($matches[0])." matches found</h2>");
    // print_r($matches);

    $patternz = array();
    $replacementz = array();
    foreach ($matches[0] as $key => $value) {
      $pat = '/'.$value.'/';
      $val = "unique-string-seahorse".(strval($key)+1);
    
      array_push($patternz, $pat);
      array_push($replacementz, $val);

    }

    $combined = array_combine($patternz, $replacementz);
    $combined = array_reverse($combined);
    foreach ($combined as $pat => $val){
        $text = preg_replace($pat, $val, $text);  
    }

     $updatedText = preg_replace('/unique-string-seahorse/', 'fn', $text);
     return $updatedText;
}



// get file contents
$options = getopt("f::");

if ($options) {
    $filename = $options["f"];
}
else {
    $filename = "input.md";
}


$maintext = file_get_contents($filename);
$textArray = explode("# Footnotes", $maintext);
$newfile = "";

foreach($textArray as $key => $value){
    if ($key == 2){
        $value == substr($value, 12);
    }
    $newfile .= updateFootnotes($value);
}

 $output = fopen('output.md', "w+");
  fwrite($output, $newfile);
  fclose($output);
  echo ("done");


?>