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1. Select a working set in Target Explorer view. 2. Right-click it and select "New Other..." from the pop up menu. 3. Select "File" in the wizard selection page and click next. 4. Select a target which has a file system and click next. 5. Expand the tree for selecting folders. Notice that "hidden" and "system" files are still visible even these two filters have been turned on.
Fixed at the commit: http://git.eclipse.org/c/tcf/org.eclipse.tcf.git/commit/?id=d40663577799772460aebf7ba9bf115f09b61940