I ran into some issues here when switching our tests to use
`.jj`-internal git repos. For example, the `std::fs::copy()` calls
started failing, which may be related to #2103. I think one problem is
that we could end up calling `merge_directories()` twice for the same
directory. This patch fixes that by deduping the paths we call with,
and makes the function assume that the output directory doesn't exist.