How to set custom upload directory per user after moving content directory

With credits to petermolnar via irc://freenode.net/wordpress I can answer my own question. The key is to set an upload-dir filter in the theme’s functions.php:

function per_user_upload_dir( $original ){
    // use the original array for initial setup
    $modified = $original;
    // set our own replacements
    if ( is_user_logged_in() ) {
        $current_user = wp_get_current_user();
        $subdir = $current_user->user_login;
        $modified['subdir'] = $subdir;
        $modified['url'] = $original['baseurl'] . "https://wordpress.stackexchange.com/" . $subdir;
        $modified['path'] = $original['basedir'] . DIRECTORY_SEPARATOR . $subdir;
    }
    return $modified;
}
add_filter( 'upload_dir', 'per_user_upload_dir');