From FDT Documentation
FDT as various kind of refactoring available. One useful one is Move Refacotoring. When developers move a file from one package or folder to another, FDT will detect it and successfully update all necessary references to it. This way your code never gets broken even as you move classes around.
Using The Explorer
One way of using move refactor is to click and drag files via the explorer.
Using The 'Move...' Command
Another, more precise, way of moving files around is with the 'Move...' menu option. This allows you to preview the changes to your code before implementing the move.