crates.io-index repository consistency; registry-watcher fails for private repos

[gregvirgin]

I noticed that in some places it is presumed crates.io-index is a bare git repository, while in others it is not. This is creating some interesting issues:

• At some point, I suspect the index was converted to being bare post-setup. This presumably had an effect on crates-index-diff_last-seen
• Performance of Updating crates.io index is erratic (though not problematic).
• daemon --registry-watcher=enabled never finds any new crates. It shows Checking build queue and Queue is empty, going back to sleep repeatedly with no logs from the diff appearing.

It may be necessary to work off of a private repo (we use cloudsmith.io) to fully replicate these issues, however the discrepancy with crates.io-index is pretty clear without needing to.

[gregvirgin]

Happy to help debug