- Filesystem.php

     1. Created a new `Filesystem::replace()` method that atomically
        replaces a file if it already exists.

  - PackageManifest.php

     1. The Filesystem::get() call in PackageManifest::getManifest() no
        longer has to use an exclusive lock because the packages.php
        manifest file will always be replaced atomically.

     2. Use the new Filesystem::replace() method in
        PackageManifest::write()

Actually, changing owner won't work anyway if you're not root, so remove
that.

Remove chmod() and chgrp() because it's a bit overkill and probably
won't work properly on Windows.