I've looked through the Preferences window a few times to ensure I didn't miss a setting, but 2016 no-longer seems to remember the collapsed/expanded state of the File Explorer TreeView nodes for a project when WeBuilder is restarted. At least, I think the state was remembered in 2015? If not, feel free to move this post to the Requests area.
A(nother) feature request: having Activate Folder of Current File toggleable so the File Explorer automatically follows the currently active document tab.
Edit: Activate Folder of Current File doesn't appear to have a corresponding entry within the Keyboard Shortcuts window.