Move apply-patch file changes into turn items

[pakrym-oai]

Why

Apply-patch file changes are now part of the core turn item stream, so v2 clients can consume the same first-class item lifecycle path used by other turn items instead of relying on app-server-specific remapping from legacy patch events.

What changed

• Added a core TurnItem::FileChange carrying apply-patch changes and completion metadata.
• Updated the apply-patch tool emitter to send ItemStarted / ItemCompleted with the new FileChange item while preserving legacy PatchApplyBegin / PatchApplyEnd fan-out.
• Updated app-server v2 conversion to render the new core item directly and stopped event_mapping from remapping old patch begin/end events into item notifications.
• Kept thread history reconstruction based on the existing old apply-patch events for rollout compatibility.

Verification

• cargo test -p codex-protocol -p codex-app-server-protocol
• cargo test -p codex-core --test all apply_patch_tool_executes_and_emits_patch_events
• cargo test -p codex-app-server bespoke_event_handling

[owenlin0]

nice, this makes the app-server layer simpler too!

at some point (maybe once we migrate everything to CoreTurnItems?) we should persist these in the rollout instead of the legacy EventMsg ones