Linus Torvalds <torvalds@linux-foundation.org> writes:

quoted text
> That's why tying "--git" together with any prefix handling is wrong: 
> because it's a totally different issue. It's true that "git-apply" right 
> now doesn't understand these things, but assuming we want to teach 
> git-apply to apply to subprojects eventually (we do, don't we?) we'll 
> eventually have to teach it.

That's all correct but

 * currently diff does not recurse, nor apply does not apply
   recursively;

 * "git diff" that comes with 1.5.4, if we do not do anything,
   can produce a diff that will be rejected by the stricter
   check "git apply" has when used with --no-prefix and friends;

 * submodule aware versions of "git diff" can be told to add
   "--mark-as-git-diff" when it passes "--src-prefix=a/git-gui"
   and "--dst-prefix=b/git-gui" when it recurses internally, to
   defeat what my proposed patch does.

So I think it makes more sense to mark output as a non-git diff
when custom prefix is used in the version we are going to ship
as part of 1.5.4.
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