Brassaia: Backport parts of Irmin v3.9

What

(depends on !12794 (merged))

Backports some of the changes from Irmin v3.9 into Brassaia.

• https://github.com/mirage/irmin/pull/1839
• parts of https://github.com/mirage/irmin/pull/2267 (everything but the test changes as they are not yet forked into Brassaia)

Unmerged PRs from Irmin might be of interest too:

• https://github.com/mirage/irmin/pull/1864
• https://github.com/mirage/irmin/pull/2014
• https://github.com/mirage/irmin/pull/2042
• https://github.com/mirage/irmin/pull/2132

Why

How

Manually testing the MR

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