I wrote to FSF about possibility of storing binutils patches and such things in the source tree. Here's their answer in full:
> Hello, Peter, and thank you for contacting us!
>
> > I am working on MINIX operating system, which has BSD-alike license, see
> > here:
> >
https://git.minix3.org/index.cgi?p=minix.git;a=blob;f=LICENSE;h=a119efa5f44dc93086bc34e7c95f10ed55b6401f;hb=HEAD
> >
> > In the MINIX source tree, there are some patches for
GNU binutils, GCC, and
> > some other
GNU packages which are used in the build process and not
> > included in distribution. Obviously, these patches are
GNU GPL-licensed,
> > and MINIX license states this in 'Aggregated Software' section.
>
> As far as I understand, Binutils and GCC are standalone packages,
> they don't form a "larger work" with the OS (GCC has a dedicated
> exceptions for its parts that may form such work with its output),
> so the passage about "aggregates" in Section 5 of the GPLv3 [0] is likely
> to apply; this may or may not be the case for other
GNU packages.
>
> [0]
https://www.gnu.org/licenses/gpl-3.0.html#section5
>
> > My question is: Is this legal to store these patches in the source tree?
>
> I assume that the patches are equivalent to the source code, that is,
> it's trivial to get the patched source tree from them. If this is
> correct, then their distribution is to comply with the Section 5
> of the GPLv3. It depends on the actual patches whether it does.
>
> If they are not equivalent to the source code, then they qualify
> as object code in terms of the GPL, and fall under the Section 6.
>
> > I will post your answer to MINIX group if you don't mind.
>
> If you do, please post our response in full, so that it isn't
> taken out of context.
>
> --
> I am not a lawyer, this is not a legal advice.
> The services of the GPL Compliance Lab are made possible by
> donations from people like you. Please consider supporting us
> today by becoming a member [
https://my.fsf.org/join] or by making
> a donation [
https://www.fsf.org/donate].
As long as our patches are source code, we are fine.
N.B.: THIS IS NOT A LEGAL ADVICE
Best regards,
Peter