Improved practical use of Composer

In the practical use of Composer I had two problems:

1. I can't use my own Magento Theme with Composer, because Composer can't link it to app/design/frontend/boilerplate/ as long as it is a symbolic link, so I have fix it in the modman file.

2. I can't run the "composer update" command as long as I use my own index.php or .htaccess, so I have made it optinally.

Cheers!