root/clean.php

<?php
/**
 * Gets a list of files from a directory.
 * Recursively descends into subdirectories.
 * Only lists files starting with a dot (not inluding .svn files).
 * 
 * @todo replace this with shell script `find . -type f -name "\.*"` ...
 * be sure to check exit status.
 * 
 * @todo replace with `find . -type f -name "\.*" -exec rm {} \;` instead?
 * 
 * @todo replace with `find . -type f -name "\.*" -print -delete` instead?
 * 
 */
function getBadFiles($base, $dir = null)
{
    if ($dir === null) {
        $dir = $base;
    }
    
    $list = array();
    foreach (scandir($dir) as $name) {
    
        if ($name == '.' || $name == '..' || $name == '.svn') {
            // skip!
            continue;
        }
        
        $result = "$dir/$name";
        
        if (is_dir($result)) {
            // recurse into the subdirectory
            $sub = getBadFiles($base, $result);
            $list = array_merge($list, $sub);
        } else {
            // only get names starting with a dot
            if (substr($name, 0, 1) == '.' ||
                substr($name, -1) == '~') {
                $list[] = $result;
            }
        }
    }
    
    asort($list);
    return $list;
}

// now actually delete matching files
foreach (getBadFiles('.') as $name) {
    echo "$name\n";
    unlink($name);
}