Refactoring code

[jasmin-guven]

This is the main issue to track the refactoring of this code.

To do

• refactor: rename repo to meze #35
• feat: input and output to prepare.py should be replaced with JSON #36
• refactor: replace prepare.py with meze command #37
• feat: add alchemlyb analysis to main #42
• feat: add option to add angle restraints to restraint model (make default) #38
• feat: add ZAFF modelling option #39
• build: make pip or conda installable #40
• add documentation with examples #41