The drush directory is intended to contain drush configuration that is not site or environment specific.
Site specific drush configuration lives in sites/[site-name].
You should add the Drush aliases for any remote environments (such as Acquia Cloud) to the sites directory. This allows developers to access remote environments using simple aliases such as drush @mysite.dev uli. Note that if you are using Acquia Cloud, developers can also download these aliases manually from their Insight account, but providing them with the project makes everyone’s life a little easier.
You can find these aliases for Acquia Cloud sites by logging into https://accounts.acquia.com and going to the Credentials tab on your user profile. Download and place the relevant alias file into sites.
Note that if the version of Drush that your project uses is significantly ahead of the version available in the remote environment, you’ll need to manually set $drush_major_version at the top of your alias files to match the version of Drush on the remote environment. For instance, at the time this document is being written, Drush 9 is in development and only Drush 8 is available on Acquia Cloud, so you’d want to add the following to the top of your aliases: $drush_major_version = 8;
It can be helpful to define aliases for a local environment such as @mysite.local. This creates consistency with how aliases are already defined for remote environments (such as @mysite.dev, @mysite.test, and @mysite.prod). To create these local aliases, copy example.local.aliases.drushrc.php to local.aliases.drushrc.php and modify the default values as appropriate for your project.