I used to be able to see my .js files under each folder in the Repositories section on the left hand corner of Smartgit.
But now I only see the folders, is there a setting to turn on to see the files?
As mstrap mentioned it is not possible to see files in the Repositories view/windows.
You have to look in the Files view/windows (screenshot *1). If it is not visible you can get it by pressing Ctrl +Shift+2. If the are not shown there maybe your filter settings are not correct (screenshot *2).