Multi-Store Setup with Sub-Directory on Nginx PHP-FPM

I have addressed this issue with a quick little bit of PHP

https://github.com/joekersh/magento-multistore-robots

.htaccess

RewriteRule ^robots.txt$ /robots.php [NC,L]

robots.php

<?php

// Find VirtualHost name and define as variable

$url = $_SERVER['SERVER_NAME'];

// Define multi-store websites url

$website1 = "website1url";
$website2 = "website2url"; 
$website3 = "website3url"; 
$website4 = "website4url";

// Test for requested website then display relevant robots.txt content

if (strpos($url,$website1) !== false) {
    include 'rbts-depend/website1.php';
}

if (strpos($url,$website2) !== false) {
    include 'rbts-depend/website2.php';
}

if (strpos($url,$website3) !== false) {
    include 'rbts-depend/website3.php';
}

if (strpos($url,$website4) !== false) {
    include 'rbts-depend/website4.php';
}



?>

rbts-depend/website1.php

<?php

$content = 
"User-agent: *
# INSERT ROBOTS CONTENT HERE"
;

echo $content;
?>

and so on...

one way to handle this would be

1. create a public folder into your magento root
2. inside that public folder you can create your subfolders us, nl
3. and inside of those subfolders you can clone index.php and .htaccess files and create symlinks to ../../skin, ../../errors, ../../media
4. at this point you can edit .htaccess freely and index.php freely to set your store scope and include the right resources and you can safely commit this to version control as you are not affecting any core files and can manage all configurations from one place.
5. optionally you can hide the whole magento root folder out of public_html folder on your server where domain is pointed and just symlink the folders (ln -s /path/to/public/us us/) to this destination