This issue has been bugging me for a while and I just worked out how to solve it: if you’re using NetBeans and add some files to the project outside NetBeans (like copying and pasting in Finder/Explorer) then they don’t show up in the list of files in the projects tree view.
OK, it’s incredibly simple and I’m annoyed I didn’t find this sooner:
Select “Scan for external changes” from the “Source” menu.
After the scan the new files will show up.
As I write this post, I’m using NetBeans 7.0 on Mac Snow Leopard. I know I had similar issues with trying to work out how to get the site tree to refresh in earlier NetBeans 6.9 but as I don’t have it installed any more I don’t know if the scan for external changes option is available in earlier versions.