refactor: move `Makefile` to root directory #684

Job	Run time
rust-tests (ubuntu-22.04)	2m 16s
python-tests (ubuntu-22.04, 3.9)	1m 52s
integration-tests	2m 27s
python-tests (ubuntu-22.04, 3.12)	1m 54s
python-tests (macos-14, 3.12)	1m 47s
Publish coverage reports to codecov.io	1s
	10m 17s

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