Under normal usage, what is the difference between these two commands in the File menu? Cmd-W closes the entire project too, if there are no floating windows with focus. I thought I remembered an item in the change list stating that Cmd-W would no longer close the project, but I must have been hallucinating.
Cmd-W closes the active window or panel. This may be the keywords HUD, snapshots panel, or any other active window that has a “close” button (which therefore excludes only the full screen window). If the main project window is active, then Cmd-W closes the project. Shift-Cmd-W, on the other hand, closes the project regardless of any other panels having the focus. This is standard behaviour for project-based apps (based, in fact, on Xcode). The change you are thinking of was that previously there was only a Cmd-W, and this always closed the project, which meant that users were sometimes going to close the keywords HUD in this manner and finding that the project closed.
Hope that clears things up!