If there is a directory or JAR file mounted in Filesystems because you need it on your classpath, but you will not be modifying it, you can hide it. In the Explorer, right-click the filesystem's root node and choose Properties. On the property sheet, change the Hidden property to True.

To redisplay the filesystem, choose Project | Settings from the main menu, expand the Filesystems Settings node, select the filesystem, and set the Hidden property to False.