In Visual Studio 2008, I can see all my project files in my Solution Explorer, and these files exist in an actual diectory.
However, if I add a file to that directory
These days you can use the TF command line to do this.
tools, command line, developer command prompt; or often you can find a shortcut under your start menu's Visual Studio Tools folder).tf add * /recursive to select everything / push it all to the project. Other options documented in the tf docs.Team Explorer pane's Pending Changes section to make any adjustments you may wish via the UI.