EDE can work with your Automake files in two different ways. If you write your automake files, they will read and configure them using the user interface.
If you prefer, you can do EDE all for you. First create your first C file, and then when it is on disk, do:
Mx ede-new RET Automake RET
then, in the project / project options menu, add a goal, such as "program."
If you fill out your C file, you can select Project-> Build-> build currentproject from the menu, and it will create and configure everything that Automake needs to do this, in addition to running all the misc automake required commands.
Finally, there is the “run” option to launch your program.
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