Replace Makefiles with bash scripts

[phsauter]

Replace all Makefiles with basic shell scripts except for the sw/ where one Makefile should build the software binaries.
The idea behind this is to create simple scripts that people can copy-paste line-by-line into a terminal to better understand what each step does.
As such the shell scripts should be held on the simpler side. Functions are okay as long as each one performs one closed step in the process and functions calling more functions should be avoided.