If you have worked on Drupal before, you have likely heard the following advice given about where you should put your modules:
The fact that this is a common suggestion does not mean it is the only suggested method, or even the best. There are several competing conventions for how you should organize modules. Each has its advantages and disadvantages.
This advice is convenient for situations in which there is only one site. But for multi-site configurations, things get more complicated.
sites/all/ directory houses data that is shared among all of your sites. ...