Update to irmin.3.3.1

This MR aims to update irmin from 3.2.2 to 3.3.1. To do so, small API changes are needed.

Additionally, it bumps the version.json of the storage from 0.0.8 to 1.0 and introduces an upgrade command, as the format is not backward compatible. Note that the upgrade command is almost instantaneous.

Associated opam repo MR: opam-repository!326 (closed)

Manually testing the MR

Try the upgrade command by hand.

Run and monitor a node to make sure the context is consistent.

Checklist

• Document the interface of any function added or modified (see the coding guidelines)
• Document any change to the user interface, including configuration parameters (see node configuration)
• Provide automatic testing (see the testing guide).
• For new features and bug fixes, add an item in the appropriate changelog (docs/protocols/alpha.rst for the protocol and the environment, CHANGES.rst at the root of the repository for everything else).
• Select suitable reviewers using the Reviewers field below.
• Select as Assignee the next person who should take action on that MR