diff and patch do not handle some changes to directory
structure. For example, suppose one directory tree contains a directory
named `D' with some subsidiary files, and another contains a file
with the same name `D'. `diff -r' does not output enough
information for patch to transform the the directory subtree into
the file.
There should be a way to specify that a file has been deleted without
having to include its entire contents in the patch file. There should
also be a way to tell patch that a file was renamed, even if
there is no way for diff to generate such information.
These problems can be fixed by extending the diff output format
to represent changes in directory structure, and extending patch
to understand these extensions.