Instead of always including empty directories in `glob()`, make it an
opt-in behavior because technically it's a breaking change to include
them by default.
There are some edge-case situations where a dependency or build process is expecting an empty directory to exist, and this expectation would fail currently because `glob()` does not return directory entries.
So update `glob()` to return entries for empty directories, which are also re-created properly when passed to the `download()` function.
