Fix issues related to git updates

We observed that after updating the git repo in a test, unless we waited
for 1s, we got intermittent cases where a subsequent update of the git
source would not pick up the changes.

We observed this both with the git CLI and the branch using libgit2.
There may be a better solution, but we did not find it.
auto merge of #378 : wycats/cargo/fix-git-issues, r=alexcrichton