Java for Mac is not one application, but an entire suite of interactive files, mostly compressed. The extension .smi is not a part of Java per se, but part of the installer volume you downloaded. An .smi is either a self-mounting image file (double-click and it mounts a volume on your desktop) or a small file associated with RealPlayer, which we obviously aren't dealing with here. If you downloaded an .smi file and then put it somewhere without mounting it, then you aren't installing anything. Double click on this file, and magic will happen!

The installer puts several folders in different locations:MRJ Libraries, for instance, is in system>extensions; the Mac OS Runtime for Java folder does indeed go into Applications>Apple Extras; and the Cache goes into Application Support. Don't worry about where the installer dumps these. It knows what it is doing. Joakim and I are talking about different parts of Java.

Filesharing has nothing to do with Limewire. Unless you have this utility properly configured, however, you should keep it off when you are online.