I'm not going to comment on the validity of this specific case, but "open source" doesn't automatically mean "protected from copyright law infringement".
They have to do it to protect trademark, but not copyright. I'm not sure there's any real copyright claim to be made here. The DMCA does have provisions against reverse engineering etc. It's not clear to me from this notice exactly what's believed to be infringing other than the Trademark claim, which is pretty straightforward (and easily gotten around).
> The DMCA does have provisions against reverse engineering
Here in the EU reverse engineering is allowed and even if you sign a contract saying you won't reverse engineer something you've still got the right to do it.
How would the DMCA comply with this, would anyone be able to shut down legally reverse engineered code on GitHub?
I always wondered, if a company doesn't really want to protect their trademark (too much hassle), but has to, can't they just grant people a (temporary, revokable) right to use the trademark pro forma?
I remember seeing a company (something Linux-related) that had a very strict trademark policy, and they did sue people who used their logo or their name, or event something different but similar. But their web site had a form where you could just enter your email address and name, and it would say oki-doki, you may now use our trademark as you like, until we say otherwise.