At some point all files in my working copy got marked with \"S\" symbol as shown below:
$ svn st
M S AclController.php
S InstallationController.php
This means that you've switched from one working copy to another, for example you've checked out a working copy, then swapped it over to be comparing against a code branch. Take a look at the SVN book for details on how to undo this.
In my case two sub-directories in the branch were deleted in the trunk. I switched from trunk the branch from the top level directory, and then moved back to trunk and experience the problem with those sub-directories are now in status S
.
I used the answer by @ahnbizcad as a guideline. From the parent directory (which is itself under the top level directory) of the sub-directories:
svn sw <branch_url>
svn sw <trunk_url>