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I apologize if someone has already reported this -- I couldn't find a duplicate. If you create a new patch, and choose "Include new files in patch", Eclipse (very un-intuitively) ignores new files which exist in new directories. Please, either fix the wording to indicate that new directories will be ignored, or (preferably) include the new files in the patch.
Even though this is a CVS limitation, we should be able to support the inclusion of new folders, especially considering we were able to do it for new files. We should investigate providing this for 2.2
*** Bug 19149 has been marked as a duplicate of this bug. ***
Created attachment 5216 [details] Implementation for patching new directories
Supports all three diff format, unified, context and standard. (Of course, only the unified format can be consumed by the Apply Patch action)
Created attachment 5218 [details] Minor improvements on initial patch
Released to HEAD by Michael V.