Keeping directory structure when creating frameworks in xcode
Use Copy Files instead of Copy Headers in the Build Phases UI.
Create a separate Copy Files (Editor -> Add Build Phase) for each output folder needed.
If you cannot use a folder reference because the folders contain non-header-files, too, which you don't want to copy, add a Run Script build phase instead:
cd "${SRCROOT}/path/from/project/root/to/headers"echo 'Copying headers into Framework..'for H in `find . -name "*.h"`; do echo "copying ${H} to ${BUILT_PRODUCTS_DIR}/${PUBLIC_HEADERS_FOLDER_PATH}/${H}" ditto "${H}" "${BUILT_PRODUCTS_DIR}/${PUBLIC_HEADERS_FOLDER_PATH}/${H}"doneThat will copy all .h files from the path you cd'd to into YourFramework.framework/Versions/A/Headers just like marking them as public would.
It seems that this is not currently a built in feature of xcode, so you must revert to scripts to copy files recursively (presumably selecting only header files): How can I preserve subgroups when changing role to public in Copy Headers build phase in XCode?
Here's a discussion about how to accomplish just that: http://www.cocoabuilder.com/archive/xcode/259185-copy-headers-that-preserves-subdirectory-structure.html