Renames all files in a folder having an extension to a sequential numeric name preserving existing numerically named file names

gistfile1.txt

<?php

$baseDir = $argv[1];
if (false === is_dir($argv[1])) {
    die ("$baseDir is not a directory");
}

// get all files with an extension
$allFiles = array_filter(
    array_map('pathinfo', glob("$baseDir/*")),
    function($finfo) {
        return isset($finfo['extension']);
    }
);

// init map of available numbers
$newFiles = array_pad([], count($allFiles) + 1, null);
unset($newFiles[0]);

// fill existing numbers
foreach ($allFiles as $key => $file) {
    $index = $file['filename'];
    if (array_key_exists($index, $newFiles)) {
        unset($newFiles[$index], $allFiles[$key]);
    }
}

// merge
$newFiles = array_combine(array_keys($newFiles), $allFiles);

if (count($newFiles) === 0) {
    echo 'No files need to be renamed', PHP_EOL;
    exit;
}

// rename
foreach ($newFiles as $newNumber => $file) {
    $source = sprintf(
        '%s/%s',
        $file['dirname'],
        $file['basename']
    );
    $target = sprintf(
        '%s/%s.%s',
        $file['dirname'],
        $newNumber,
        $file['extension']
    );
    printf("Renaming %s to %s\n", $source, $target);
    copy($source, $target);
    unlink($source);
}