I have standard source code package under Linux which requires to run
./configure
make
to compile it (and it works ok).
Mostly thes
Create a new project, make sure to uncheck the "Use default location" option while doing so. Add your source tree path in the location field. Now select "Makefile Project" in the project types window.
In "builder settings" (Project>Properties), uncheck the "use default build command" and add:
make -f /
If your makefile is named otherwise, you can change it here.
To run your application, add the application in Run Configurations. See full instructions here.