Worktree not fully populated in certain situations

When Collector initially creates the worktree for a content source repository, and when it subsequently does a checkout from one ref to another, it can leave the worktree in an incomplete state (often not fully populated). This happens because the index and worktree it is starting from don't always match. For example, if it's moving the worktree from 5.8.x to 5.7.x, and the index is for main, it may not fully populate the worktree.

We detected this error when one of the repositories using Collector contained symlinks. isomorphic-git was reporting that it could not create the symlink. This happened because isomorphic-git was not creating all the folders, and thus the symlink call failed. But the problem is much broader than symlinks.