Fix symlinking of new projects

We weren't copying these lists, so the += was actually changing the
underlying lists.

When a new project was added to the manifest, we run _CheckDirReference
against the manifest project with share_refs=True, which added the
working_tree_* to the shareable_* lists. Then, when we load the new
manifest and create the new project, it uses the lists that already
contain the working_tree_* files, even though we passed
share_refs=False.

This happens reliably under the above conditions, but doesn't seem to
happen when syncing a fresh tree. So we've got a mixture of links that
may need to be cleaned up later. This patch will just stop it from
happening in the future.

Change-Id: Ib7935bfad78af1e494a75e55134ec829f13c2a41