Documentation conversion and pre-commit updates

Closes #28

See merge request !4

Initial approach for unifying Flag and Register

See merge request johku144/simudator!3

Refactor MiaRegister to IntegerRegister (including GUI)

See merge request johku144/simudator!2

moved all actions for the context menus to the modules, also added a signal system where the modules give the gui signals for when they want to add breakpoints or update the ui