Use `ClinicaIO` for reading and writing BIDS and CAPS files

[NicolasGensollen]

The objective is to rely on ClinicaIO for reading and writing files in BIDS and CAPS folders.

[github-actions]

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

[github-actions]

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.