The PEN tool lets you ignore files and objects. When files/objects are ignored, they are not affected by any other action taken in PEN (i.e., upload, download, delete, copy and paste, etc.). The only action that can be taken on an ignored file/object is to unignore it.
You can ignore all file types – local files (blue files), Warehouse files (grey files), and files that exist both locally and in the Project Warehouse (black files).
To ignore a file or object, select it in the left panel, right click, and select “Ignore” from the menu. When you ignore an object, the object node will be collapsed and none of the sub-directories or files within that object will be accessible.