The user.email config value contains a valid email address (the one I use at github), followed by a newline character. While debugging I tried removing the ending newline character, but to no avail.
This caused entries like these to be added to the HEAD log of a cloned repository:
0000000000000000000000000000000000000000 6ebb694db3f12503755986490984bae37c9e9e18 Kostas Stroggylos
> 1368647608 +0300 checkout: moving from master to 6ebb694db3f12503755986490984bae37c9e9e18
In the test repository working directory (LibGit2Sharp.Tests/Resources/testrepo_wd) I am able to perform git checkout -f from the command line.
I used git config to set new values without trailing newline and it seems to be ok now. I suppose the command line git trims the configuration values before using them.