Make programs are very good at keeping track of targets, files that need to be built, and the dependencies between targets. But the Make program is only as good as its inputs. If you don't tell Make about a relationship between two files, it wont discover it on its own and it'll make mistakes because it assumes it has perfect knowledge about the files and their relationships.
Usman's Law (named after a smart coworker of mine who spent months working with customer Makefiles). make clean is intended to take you back to a state where everything will be rebuilt from scratch. Often times it doesn't. Here's why.
Many build processes run for hours with build managers commonly typing 'make' and going home for the night. GNU Make's solution to this problem is parallel execution, which is a simple command-line option that causes GNU Make to run jobs in parallel using the dependency in the Makefile to run in the correct order.