Before you go head on in on such a project you should check what is already available in that regard.
So look how FlowStudio creates and maintains makefiles and how the underlying GNU tools work.

Includes should not be manually added to a makefile, just the search paths (for nonstandard ones).
Makefiles should have a "depend" target to make sure files get flagged for recompile if an include had been changed or added to a source file.

GUI part would then be more or less down to what you can do in the "Project" menu in FlowStudio and IMO it would be nice if your tool would spit out FlowStudio projects as an option.