[ENH] Separate converters and iotools in separate modules

[NicolasGensollen]

Description

This PR investigates the architectural change of having converters and iotools in their own modules instead of sharing the same clinica.iotools module.

The base idea is to have:

• the CLI clinica convert using code from the clinica.converters module
• the CLI clinica iotools using code from the clinica.iotools module
• the CLI clinica run using code from the clinica.pipelines module

Objects used in multiple modules are moved in another top-level module (at the moment it is clinica.utils although this may evolve to something better one day...).

This is in our roadmap as the first step toward maybe splitting the converters of Clinica into their separate package one day.

Things to do

• Fix all the broken unit tests
• Make sure non regression tests are passing
• Make smaller architectural improvements (especially around things related to BIDS which are still defined in multiple places....)