Dev Build 3042 is out now.
Plugins can now be overridden as expected: for example, you can override the default toggle_comment plugin by creating a file Default/comment.py under your Packages directory.
There have been some changes to atomic_save on OS X and Linux, too: situations where permissions are unable to be set on the new file, such as when editing via SFTP, will cause a regular save to be performed instead. Hopefully this will avoid some of the surprises when saving via atomic save, while still getting the benefits when saving locally.