The GitHub denied the rumors about the hack, after a strange notification that is said to have shown him source code of GitHub.com and GitHub Enterprise portals.

The "supposed" source code leaked to the DMCA section of GitHub.
The leak appears to have been made by the CEO of GitHub, Nat Friedman. However, in a message posted on YCombinator's Hacker News portal, Friedman denied that he did leakage and generally that there was some kind of hack on GitHub.
Friedman said the "leaked source code" did not cover the entire GitHub code but only the GitHub Enterprise Server. This is a version of GitHub Enterprise, which companies can run on-premise servers in case they need to save their source code locally for reasons security (but still take advantage of GitHub Enterprise capabilities).
Friedman admitted that this source code is not due to a current hack, but was leaked months ago due to an error platform (GitHub engineers "mistakenly sent a portion of the GitHub Enterprise Server source code to some customers").

However, Friedman promised that GitHub was going to fix two errors who seems to have taken advantage of the person to do this now leakage. With the correction, it will prevent unauthorized users to link their code to other people's projects through fake identities.
"In short: everything is fine, the situation is normalSaid Friedman.
This is not the first time this has happened
This is not the first time this has happened to GitHub. One of the two bugs was used a few days earlier when a security researcher attached the source code of the youtube-dl library to the DMCA section of GitHub.
The leak seems to be one form of protest against GitHub's decision to ban those who use it youtube-dl library.
According to ZDNet, the person who made the leak did not explain his actions, but is believed to have leaked the source code of GitHub Enterprise Server to protest the removal of youtube-dl, a project that allows users to download audio and videos from YouTube and others services (abolition was decided when the RIAA complained about piracy of its songs via youtube-dl).
Since last week, Hundreds of other users are re-uploading the youtube-dl code to their own accounts and cause the RIAA to denounce them as well. GitHub warned them users do not do so, as there is a risk of being banned.