I don't know about the problem, nor can I currently test it.
but the runwait.sh seems to exist (in svn) => so maybe the installer didn't set the executable flag?
have you tried chmod a+x runwait.sh
Also, you should be able to change the launcher app in "run param" from the "run" menu.
But: some launcher do not work in gdb at all.
Also if you start a console app in gdb, you may have to specify a terminal for in/output first => or you will not see anything.
If you succeed with a starter app, you may be fine.
If you run without starter app, by default all output goes to dev/null => see "options" form the menu; page "debugger" there is a property grid, with a tty entry.
to get a tty => launch a shell, run the command "tty" (will only be valid, until you close the shell)