refactor: remove proto types from d-engine-core Raft protocol layer

[JoshuaChi]

Background

d-engine-core uses proto-generated types (Entry, EntryPayload, LogId,
AppendEntriesRequest, VoteRequest, …) as internal Raft data structures,
creating a hard proto dependency inside the consensus layer.

#415 removed KV semantics (WriteCommand) from core. This ticket removes
the remaining proto dependency — the Raft protocol types themselves.

Goal

Replace proto-generated Raft types with native Rust structs in d-engine-core.
Serialization lives only at the network transport and WAL storage adapters.

Target state: d-engine-proto removed from d-engine-core's Cargo.toml.