Align app-server v2 guidance with split protocol modules

[andrei-hasna]

Summary:

• Point app-server v2 guidance at the split app-server-protocol/src/protocol/v2/ module directory instead of the removed monolithic v2.rs file.
• Name concrete module examples in agent guidance, MCP docs, and the app-server experimental-field checklist.
• Refresh MODULE.bazel.lock after CI reported the Bazel module lock was out of date; the lock diff only adds generated facts for anyhow_1.0.103 and tar_0.4.45.
• No app-server schema regeneration was required because protocol/schema shapes were not changed.

Validation:

• git diff --check main..HEAD
• branch diff secret-pattern scan before push: no matches
• test ! -f codex-rs/app-server-protocol/src/protocol/v2.rs
• find codex-rs/app-server-protocol/src/protocol/v2 -maxdepth 1 -type f | sort | sed -n '1,60p'
• git grep -n -E "app-server-protocol/src/protocol/v2\\.rs|protocol/v2\\.rs" HEAD -- .codewith CODEWITH.md AGENTS.md docs codex-rs ':(exclude)codex-rs/target/**' ':(exclude)codex-rs/app-server-protocol/schema/**': no matches
• just test-fast -p codex-app-server-protocol: 262 passed
• bazel mod deps --lockfile_mode=error with redirected /tmp caches: passed

Notes:

• In this OpenLoops sandbox, .codewith/ is bind-mounted read-only, so the local working-tree file cannot be rewritten. The committed tree was updated and validated directly with git show HEAD:.codewith/CODEWITH.md and git grep HEAD.
• Local Bazel commands needed redirected caches because the sandbox cannot create the default Bazel cache under ~/.cache.