If you want Linux to boot in CLI mode you need to set the default runlevel in /etc/inittab . Usually CLI mode is 3. Graphical runlevel is usually 4 or 5.
There should be a line such as
Where 3 is the runlevel. The file should give you details regarding the runlevels on Fedora.
But I'm curious... what kind of application is that, and why is it needed? Why not use the standard bash or sh, and then launch that program? Depending on that, changing runlevels might make it work or not...