I'm not sure about sites listed in the features.  But in 3.5 you can add repositories using the p2.inf (http://wiki.eclipse.org/Equinox/p2/Customizing_Metadata).

I would look something like this:
instructions.configure=\
addRepository(type:0,location:http${#58}//download.eclipse.org/eclipse/updates/3.5,name:The Eclipse Project Updates);\
addRepository(type:1,location:http${#58}//download.eclipse.org/eclipse/updates/3.5,name:The Eclipse Project Updates);

One is for the metadata, the other for artifacts, note that ':' are escaped as ${#58}.

The wiki page about customizing metadata is new 3.5 support when you are using the publisher.  The 3.4 style p2.generate.metadata integration in pde.build uses the old metadata generator.  Here p2.inf is only supported for bundles, and only the "instructions" properties work. It should be placed beside the manifest of one of the bundles in your product and it needs to be included in the binary bundle.  It will work for adding repositories, but you can't do all the other cool stuff in there.

In 3.5, PDE/Build has better p2 integration.  If you use the new "p2.gathering = true" support, then you can use everything else described on that wiki.

Check out new docs at http://help.eclipse.org/galileo/index.jsp?topic=/org.eclipse.pde.doc.user/tasks/pde_p2_builds.htm
and also in the help of your 3.5RC4 eclipse.

-Andrew

msacarny wrote:

We have an RCP-based, feature-based product using SDK 3.5RC4. We include our main feature and Eclipse features such as the CDT in the product. Although I specify an Update Site URL in our feature.xml, when I run the built product and open Window, Preferences, Install/Update, Available Software Sites, no sites at all are visible.  I would like Available Software Sites to come up with our update site listed and enabled, and used for Check for Updates. I don't want other sites, like CDT sites, listed or enabled. How is this done?

We build headlessly using ant script and PDE to build our product and its repository, then p2.director to install the repo into the product, as in Eclipse 3.4.

Thanks!
MSacarny