Currently if you make any changes in the Library folder on the file system while the tool is running, you need to manually refresh the library. It should detect this and refresh automatically.
One approach is to observe the file system. Java 7 provides this, see
java.nio.file.WatchService. There are also several third-party libraries. However not sure how robust this is on the various platforms. I think it polls on OS X.Alternatively the tool could asynchronously do a partial or complete refresh when you select or expand library nodes, and when the window receives focus.