This PR renames `tools/Makefile.*` to have the `.mk` extension. This PR also updates `README.md` and other files that references the other files.
Note: Skipped Makefile.host for this PR since it caused failures in CI for the sim build

By using a standard extension for Makefiles (https://www.file-extension.info/format/mk), editors will auto-format files.
This change will also improve developer ergonomics when searching for specific files

Verified locally that build still works, CI will verify more!