here a simple little cli script that has the guts of what youre
trying to accomplish.
NOTE: this is not a comprehensive solution :)

<?php
$srcDir = $argv[1];
$destDir = $argv[2];

if(is_dir($srcDir) && is_dir($destDir)) {
    $dirHandle = opendir($srcDir);
    while($curFile = readdir($dirHandle)) {
        if(empty($curFile) || $curFile == '.' || $curFile == '..') {
            continue;
        }
        rename("$srcDir/$curFile", "$destDir/$curFile");
    }
}
?>

-nathan

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