Cleanup flags in the codebase

Context

Based on !5452 (merged) and !5510 (merged)

The MR makes the protocols use :standard flags with additional disabled warnings (instead of discarding :standard flags).

The effect is that additional flags are now present when compiling with dune dev profile (that is: -strict-sequence, -strict-formats, -short-paths, -keep-locs).

We disable warnings starting from the warnings set used by dune defined in %{root}/dune instead.

warn-error no longer needed, warning are fatal with the dev profile and non-fatal otherwise.

I was told we don't want do use :standard because we are afraid dune could pass flags that could alter the semantic. If this is really something we are afraid of, we should also consider not using standard for other flags (ocamlc_flags, ocamlopt_flags, link_flags, ...)

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