chore(build): remove Makefile and associated build processes

This commit deletes the Makefile, which was previously used for various auxiliary tasks like cleaning directories, downloading bibliography files, running pre-commit checks, and converting Juvix files to Isabelle theories. The removal may suggest a move towards a different build system or process consolidation that no longer requires these steps. Ensure that any functionality needed from this file is replaced or handled elsewhere if still necessary.

Author: jonaprieto