Auto merge of #4060 - alexcrichton:nobare, r=matklad

Auto merge of #4060 - alexcrichton:nobare, r=matklad

Don't use a bare checkout of the index

Both old and new Cargo share the same index, so be sure to maintain
compatibility by initializing a non-bare repository for the index. Note that
a nightly Cargo still won't check out the index, but when an older Cargo comes
along and tries to check it out then it'll work.

Closes #4058