Always open a file in a specific program
If you don't mind specifying InDesign 5.5 every time, then this command line should work:


  open -a 'InDesign 5.5' myfile.indd


If you're going to do this often, you can wrap it in a shell script or bash function like


  function indd() { open -a 'InDesign 5.5' "$@" ; }


Then you'll be able to simply say


  indd myfile.indd