append url parameters to all links

1. Track Affiliate via Cookie

To track the affiliate source you can use a Cookie for internal tracking. In that case you only need to modify external links.

add_action( 'plugins_loaded', 'so265278_affiliate_check' );

function so265278_affiliate_check() {
    $is_affiliate = ! empty( $_GET['ref'] );
    if ( $is_affiliate ) {
        setcookie( 'affiliate', $_GET['ref'], MONTH_IN_SECONDS );
    }
}

Now you can always check the affiliate source in your theme/plugins like this:

function get_affiliate_source() {
    if ( ! empty( $_GET['ref'] ) ) { return $_GET['ref']; }
    if ( ! empty( $_COOKIE['affiliate'] ) ) { return $_COOKIE['affiliate']; }
    return false;
}

// ...
echo 'Affiliate source: ' . get_affiliate_source();

---

2. Replace links on page

Modifying (the external) links is a bit tricky. If you need to modify ALL links then you can use the shutdown hook and use a regex to replace all links.

ob_start(); // I think WP does ob-buffering by itself. You can try to remove this line...

add_action( 'shutdown', 'so265278_shutdown' );

function so265278_shutdown() {
    $html="";

    while (ob_get_level() > 1) {
        $html .= ob_get_clean();
    }

    // replace the links here...

    echo $html;
}

Of course you need to have a good regex to replace all the correct links on your page.

$regex = '#(<a.*?href=["\'])(.*?)(\2.*?>)#i';
$html = preg_replace_callback( $regex, '_modify_link', $html );

function _modify_link( $match ) {
    $url = add_query_arg( 
        array( 'ref' => get_affiliate_source() ), 
        $match[2] 
    );

    // Return the full `<a href...>` tag:
    return $match[1] . $url . $match[3];
}

---

Better solution (different approach)

The above shutdown handler is not the most efficient solution, as it will parse every request, also on wp-admin pages. It would be better if you have a specific function to create the external links with the correct markup.

Linke this:

function show_external_link( $url, $label ) {
    $affiliate = get_affiliate_source();

    if ( $affiliate ) {
        $url = add_query_arg( 
            array( 'ref' => get_affiliate_source() ), 
            $match[2] 
        );
    }

    printf(
        '<a href="https://wordpress.stackexchange.com/questions/265278/%1$s" target="_blank" rel="nofollow" class="external">%2$s</a>',
        esc_url( $url ),
        $label
    );
}

// In your theme/plugins
<?php show_external_link( 'http://www.facebook.com/', 'Facebook' ); ?>