Manifest: simplify api for flags

Context

This MR aims at simplifying the api regarding ocaml flags.

Move most arguments affecting flags into separate module/type.

• opaque
• nopervasives
• nostsdlib
• nostandard
• warnings
• warn_error

Regarding the logic

• the static flags are now only removed when :standard is used.
• -open flags are no longer enclosed inside the parens of :standard, it is semantically equivalent
  (flags (:standard -opam A)) becomes (flags (:standard) -open A)

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