What is the purpose of the Intellij Commander?

http://jetbrains.net/devnet/docs/DOC-17 :

The two-panel Commander paradigm is a way of representing a hierarchy which provides the following benefits when working with the project elements:

1. In contrast to the tree-mode views, the Commander always shows only one hierarchy level which is rather convenient in many situations (e.g. when you are permanently working only with one package and don't want or just don't need to view the entire hierarchy-tree)
2. It provides a very convenient interface for copying and moving packages/classes (i.e., when using copy/move operations in one of the two panels, the destination is automatically suggested according to the location currently expanded in the opposite panel). For details on the operations available from the Commander, please look at the popup menus that appears when you right-click on different nodes in the commander tree. These menus are context-dependent and allow different operations on the elements of different types.

If you don't use it, you can always disable the Commander plug-in in Settings | Plugins.