Proto & plugin: refactor run_operation RPC

Context

Refactor the implementation of the run_operation RPC with two objectives:

• remove functions / stop exposing private functions from Validate_operation and Apply that are exclusively needed for run_operation
• factorize as much code as possible with Main.apply_operation

Fixes part of #3245 (closed) by removing TMP_for_plugin.precheck_manager__do_nothing_on_non_manager_op. This means one less entry point to worry about in the future when we add the validation of non-manager operations.

This is also the first step listed in #3401 (closed).

This MR is on top of !5707 (merged) which fixes a minor problem with run_operation in tezt.

Manually testing the MR

Run the tezt tests on run_operation:

dune exec tezt/tests/main.exe -- run_operation

Checklist

• Document the interface of any function added or modified (see the coding guidelines)
• [N/A] 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