I would think that the switchContext() call in the plugin would handle it. I thought the reason it didn't work for me was that I don't have either a plugin or any code for switching contexts in index.php.
Susan, is it generating a full URL for you?
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It is generating a relative URL, the same as any [[~...]] tag does. With or without friendly URLs. It just seems odd that a link to resource ID 11 would not simply be able to load it without a lot of extra subfolders or plugins.