I am looking for some resources that speak about managing large C projects using make, header files, building configure files etc.
What resources are used by the community? Any good ones for beginners?
Here the list for your particular question
Instead of make can start with cmake or scons.
I would suggest that if you're able, learn about an alternative to make such as Scons. It's good for small and large projects alike, and it's Just Python(tm) so it doesn't have the horrible mangly "syntax" of makefiles.
That aside, for general project layout, you may want to read this GameDev article.
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