Compilers like GNU cc (and clang, FWIW) have a flag you can pass to have it dump GNU make compatible dependency files, and you can have it include system header

Compilers like GNU cc (and clang, FWIW) have a flag you can pass to have it dump GNU make compatible dependency files, and you can have it include system header files (I turn this on); and in the other direction, there is a feature of make designed to fetch and include files if they exist and, if not, to actually consider it a target for the current build system to quickly build, mostly for these dependency output files. If you use GNU automake--which is not at all required (I do not tend to use it, for example) but is the intention of the ecosystem--this is all set up for you (though maybe without turning on the feature for system header files to be included?). If you are having issues with C code and make not knowing the dependencies, you are using the tools wrong.