If  you are using Ctrl+Shift+T in Eclipse and have .git or .svn directory showing up it is easy to fix it without having to use another plugin for eclipse like subeclipse or egit.

Open the Properties of your project go to Resource=>Resource Filters and click on Add to add a new filter.

Now just do like this ScreenShot :

Change the *.git* to *.svn* if you like for subversion.