At the top level of Drupal there are two directories:

• module
• themes

This seems like the right place to put extra modules and themes, but it's not!

These are for core modules and themes.

When it comes time to do an update to Drupal, your custom and contrib modules and themes would be mixed up with Drupal core, making the upgrade hard work

Add all custom modules and themes to the sites/ directory:

• sites/modules
• sites/themes