Collector failing to checkout a second worktree from same repository cleanly

When Collector checks out a second worktree from the same repository, it is leaving the repository dirty in some cases. This happens because even though it is creating a new worktree, it is using the index cache from the previous checkout. This confuses isomorphic-git and causes it to create an incorrect index file. When creating a new worktree, Collector should only retain the packfile cache.