I'm not able to use the team menu item to apply patches that were generated by
gendiff.  The problem is that gendiff references a source file that doesn't
exactly exist in the source tree.

When using gendiff, you copy the original source file(s) to the same name but
with a different extension, foo -> foo.jk.  Then you modify the original file,
and then you'd call 'gendiff path/ .jk' and it will diff all the files that end
with '.jk' against the original file names to generate a patch.  The patch winds
up referencing that source '.jk' file and comparing it to the actual file in
your project space.  Eclipse balks on this because it can't find the source
file.  Patch will happily apply it.