currently, the hierarchy is flattened out, and all the headers files are copied into a single Headers directory, no matter what subfolder they were in, in my Classes folder.
This is a problem when referencing the headers, if the headers have "include" statements that reference other headers in subfolders.
in particular, this screws up BridgeSupport compilation.
From http://lists.apple.com/archives/xcode-users/2007/Oct/msg00162.html
"Try adding the folder containing the header to Xcode as a folder reference, and then add that to the Copy Headers build phase (you'll probably have to drag-drop it into the phase rather than checking the checkbox in the detail view). Folder references are the mechanism Xcode provides for preserving a directory hierarchy during a copy."