Dependencies. For example, Backbone depends on Underscore, and simply writing <script src="underscore.js"/><script src="backbone.js"/> encodes nothing about that fact. There's nothing stopping you updating Backbone to say a 2.0 that requires features in Underscore 2.0, but forgetting to update Underscore. On the other hand, bower update backbone will see dependencies: {"underscore": "^2.0"} in bower.js and update Underscore as well.