Manifest: Add linkall_lib

Context

In !4242 (merged) we convert protocol targets to the manifest. Many protocol dune files use (library_flags (:standard -linkall)). Currently, Manifest only supports -linkall in (flags), not (library_flags), thanks to ~linkall.

After carefully reading man ocamlc, it looks like the difference is very subtle but that (library_flags) is the best way to pass -linkall for libs. So we change this in this MR. The subtle difference is only in case a module is used in several libraries, which dune should prevent anyway.

This will make !4242 (merged) easier to review by having it use (library_flags) like it currently does instead of changing them to (flags).

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Checklist

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