We'll sort out an extension if the bug persists more than a day or so.
Its not just hammer. There are several reports of files missing from the /tf/ directories.
I lost my custom scoreboard layout and the Spy's Fancy Dress Mod. Yet all of my custom sounds remain. WTF?
You might want to look around and make sure all the custom models and materials that you have are still there.... Why on Earth would Valve even venture into the /tf/ directories?
What is this new "Manifest" thing. I dont remember it from before...
Manifest you can equate in similar regards to photoshop layers. They basically do instancing behind the scene, but allow you to create logical layers to place and organize however you choose. You could have a layer with just sound entities, or with one corner of a map, etc. It also allows you to easily slip up a map into chunks so that multiple people could work on sections at the same time. They are also tied into perforce, though I'm not sure if that made it out to the public release.