There is a choice with the transformation tools, a choice between performing the transformation on layers and/or guides, selections or paths and/or vectors. Shown here in the simplest of circumstances in the flip tool options. Simplest because it does not flip the guides while the other simple transformation tool, the move tool will move guides as well as layers (or guides/selections or guides/paths and/or vectors).
GIMP's transform tools include Move, Rotate, Scale, Perspective, Sheer and Flip.