Build breaks when copy of source tree is in a subdirectory?

[Mikael Magnusson <mikachu@xxxxxxxxx>]

[Skip the first paragraph if you don't care about the reason]
I have some[1] local patches, and running git rebase to update when
the upstream branch only edited one c file touches a lot of files,
causing pointless rebuilds. One nice way to avoid that is to use git
new-workdir to create a copy of the repo, do the rebase there, and
then reset in the original repo. This way only the changed files are
touched there and the rebuild is fast. Not so much an issue for zsh
but it doesn't hurt...

Anyway, if you leave this copy in a subdirectory of the repo, as in cp
-r zsh foo; mv foo zsh/foo, then rebuilds after rerunning .preconfig
and configure seem to fail mysteriously, claiming that zsh.mdd is not
a directory:

make[3]: Entering directory 'code/zsh/Src'
mkdir: cannot create directory 'Src/zsh.mdd': File exists
Src/../Src/mkmakemod.sh: 98: Src/../Src/mkmakemod.sh: cannot create
Src/zsh.mdd/Makefile.in: Directory nonexistent
creating Src/zsh.mdd/Makefile.in
make[3]: *** [prep] Error 1
Makemod:272: recipe for target 'prep' failed

I have no idea where to even start looking for the problem. The name
of my directory doesn't appear in any Makefile or error output, and
the directory it tries to create isn't in there, but in the original
repo. Obviously not super important to fix, since I can just have my
second repo be in ../foo instead, but still...

-- 
Mikael Magnusson