jDesktop = com.mathworks.mde.desk.MLDesktop.

getInstance;
jCmdWin = jDesktop.getClient('Command Window');
jTextArea = jCmdWin.getComponent(0).getViewport.getView;
cwText = char(jTextArea.getText);
You can place a callback that will update your GUI whenever new text is added to
the CW:
set(jTextArea,'CaretUpdateCallback',@myUpdateFcn)