Importing command line SBT projects into Eclipse

I have a project which works perfectly fine when I first run the bash script patch from SMT command line bash shell.

./create-this-app (which inherently calls ./create-this-bsp and 2 x ./create-this-lib).

There is also some subtle stuff going on in this patches. If I then run make download-elf, the application runs fine.

If I try and import these applications into eclipse then I lose the subtle background operations in the scripts and the file does not work.

Is there any way of importing these projects into eclipse while maintaining what is going on in the bash scripts?