I am using Visual Studio 2015, and I have a git repository cloned directly from the Visual Studio.
The recent update from Visual Studio from 2015 to Visual Studio 2015 Update 1 led to a malfunction in the git repository tracking changes menu (under 'Team Explorer' Changes).
Therefore, no commits are allowed through the application (due to the fact that MVS2015 does not recognize any changes).
Git commands used through command line are working (using Git for Windows), proving that this is not a repository-related problem ('git status' shows changes not staged for commit and untracked files, 'git add', 'git commit' and 'git push' allow to push new commits).
However, MVS seems to not be recognizing these changes.
Such problem persists with and without official GitHub extension. Uninstalling GitHub extension and using MVS already included git interface results in the same error. Therefore, the problem seems to be independent of the GitHub extension and exclusively MVS related.
This can be fixed by adding the *.VC.opendb and *.VC.db files to the .gitignore file of repository.