Improve architecture of clinica.iotools and clinica.converters

[NicolasGensollen]

This is a reminder to perform some cleaning and improvements of code when #1443 will be merged.

This is especially true around things related to BIDS which are still defined in multiple places (clinica.utils.bids, clinica.converters._utils etc...).

It's very likely that the end goal is to put all of this logic in clinicaIO, but in the mean time we can first work on grouping these things within Clinica to later ease the extraction.