TLDR: Apple will disable all your Alcatraz plugins in Xcode 8. Read this GitHub issue for more info and give Apple feedback to let them know we need a fully functioning replacement before disabling the existing extensions.
Update: This tool will re-enable extensions in your Xcode8 app.
Xcode 8 comes with some new features, like the ability to write custom extensions officially called Source Editor extensions. With Source Editor extensions, you can run code to interact, to a very limited extent, with your Xcode workspace.
Official Source Editor extensions not ready for prime time
Unfortunately, Source Editor extensions are very limited: They can only manipulate text and selections and only when the user selects them from a menu. This is only a small portion of the features provided in the existing Alcatraz plugin ecosystem for Xcode.
Unofficial plugins will be disabled when Xcode 8 is released
With Xcode 8, Apple has decided to disable all existing Xcode plugins in favor of new Source Editor extensions. However, because Source Editor extensions only provide a small portion of the features required by plugins like WakaTime, that means most existing plugins can not be converted to Source Editor extensions. Hopefully someday Source Editor extensions will be able to receive notifications from user events and run without you having to select them from a menu each time. Until then, you will unfortunately have to live without your existing Xcode plugins.
Give Apple Feedback
Giving Apple feedback by creating Radar Issues describing the plugin features you need might help improve Source Editor extensions. You can create a radar issue here. Also, this GitHub issue contains more history and a discussion from plugin developers.