TL;DR
I think that there is a bug in gclient which makes mistakenly run the prehooks for a nested DEPS file (third_party/libyuv/DEPS) which is NOT reachable by the toplevel DEPS recursedeps section.

Today I found three colleagues affected by this while running gclient sync:
________ running '/usr/bin/python libyuv/cleanup_links.py' in '/usr/local/google/code3/chromium' /usr/bin/python: can't open file 'libyuv/cleanup_links.py': [Errno 2] No such file or directory Error: Command '/usr/bin/python libyuv/cleanup_links.py' returned non-zero exit status 2 in /usr/local/google/code3/chromium

libyuv/cleanup_links.py is a prehook in third_party/libyuv/DEPS which was added recently by https://chromium-review.googlesource.com/436264 .

If I am reading everything correctly, the libyuv DEPS file is supposed to be used only in standalone libyuv checkouts.
In fact, nothing in chromium is mentioning libyuv recursedeps. In other words: it doesn't seem to me that libyuv is doing anything bad here.

Still, when syncing chrome, gclient seems to still recurse into the libyuv deps even if that is not mentioned by recursedeps in src/DEPS. I followed manually all the current recursedeps and none of them seem to reach into libyuv's.

So, unless I am missing something macroscopic, this seems to me a bug in gclient. Maybe due to the fact that libyuv's DEPS uses a prehooks section, which is used very rarely, so a bug might have slipped in there.

Also, not sure if this is related, but all three of us have a
target_os=['android']
in our .gclient config.
I manually inspected the .gclient files of all three and there is nothing unconventional (no other projects being pulled in)