fix(agent-adapter): reconcile Claude messages on reseed

[Zerlight]

Summary

• Fixes CODE-328 by reconciling Claude live-stream and history messages with the stable provider message ID.
• Prevents SWR focus/reconnect revalidation from duplicating completed responses.
• Preserves the CODE-272 behavior that keeps unmatched in-flight content during reseeding.
• Applies the runtime change only to the Claude adapter; other adapters and the wire protocol are unchanged.
• Adds regression coverage for main-agent, subagent, history, and conversation-store reconciliation.

Verification

• devenv shell -- pnpm check:ci
• devenv shell -- pnpm test — 222 files and 1,734 tests passed.
• Ran the desktop app with the debug protocol enabled.
• Verified an 80-line completed response remained single after focus and online revalidation.
• Verified a 60-line streaming response while repeatedly scrolling and triggering focus revalidation:
  • No rendered content disappeared.
  • All lines appeared exactly once.
  • No console errors were observed.

Checklist

• pnpm check:ci and pnpm test both pass (no Rust changes)
• I ran the affected surface and observed the change working
• No wire message changed; WIRE_PROTOCOL_VERSION does not require a bump
• New code and assets are my own work
• Relevant comments were updated; no documentation changes were required

[linear-code]

CODE-328

[greptile-apps]

Greptile Summary

This PR reconciles Claude live and historical messages using stable provider IDs. The main changes are:

• Uses provider message IDs for streamed text and thought chunks.
• Applies the same IDs to subagent messages and transcript replay.
• Adds tests for reseeding, message grouping, subagents, and command boundaries.

Confidence Score: 5/5

The change looks mergeable after guarding deltas that arrive without a matching message start.

Provider IDs are applied consistently across the main reviewed paths.

A resumed or partial stream can assign an early delta to stale message state. The issue is limited to streams that do not begin with the expected start frame.

T-Rex Logs

What T-Rex did

• T-Rex ran the PR tests against the parent revision 4556ef7 and observed 3 provider-ID regressions and 69/72 tests passing.
• T-Rex ran the PR tests against the PR source and confirmed all 72/72 tests passed across 5/5 files in 2.67s with exit code 0.
• T-Rex validated the notable passing cases, including provider-ID convergence across SDK/history, subagent text/thinking identity, history replay identity, snapshot-covered live-chunk deduplication, and preservation of an unflushed in-flight tool call.

_{Ran code and verified through T-Rex}

Important Files Changed

Filename	Overview
packages/host/agent-adapter/src/native/claude-code.ts	Switches live, subagent, thought, and history events to stable provider message IDs, but early deltas can still use a stale cursor.
packages/client/core/tests/integration/conversation-store.test.ts	Adds coverage for replacing buffered live chunks with a completed history message sharing the same ID.
packages/host/agent-adapter/src/tests/message-grouping.test.ts	Adds coverage for provider identity across Claude stream frames.
packages/host/agent-adapter/src/tests/claude-code-subagent.test.ts	Updates subagent identity tests and verifies that subagent frames preserve the main cursor.
packages/host/agent-adapter/src/tests/normalize.test.ts	Adds history replay coverage for provider-based text and thought IDs.
packages/host/agent-adapter/src/tests/claude-code-commands.test.ts	Updates command tests to include provider message-start frames.

Sequence Diagram

%%{init: {'theme': 'neutral'}}%%
sequenceDiagram
participant SDK as Claude SDK
participant Adapter as Claude adapter
participant Store as Conversation store
SDK->>Adapter: message_start(provider ID)
SDK->>Adapter: content deltas
Adapter->>Store: Live chunks keyed by provider ID
SDK->>Adapter: Historical assistant row
Adapter->>Store: History chunk keyed by provider ID
Store->>Store: Reconcile history and live chunks

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sequenceDiagram
participant SDK as Claude SDK
participant Adapter as Claude adapter
participant Store as Conversation store
SDK->>Adapter: message_start(provider ID)
SDK->>Adapter: content deltas
Adapter->>Store: Live chunks keyed by provider ID
SDK->>Adapter: Historical assistant row
Adapter->>Store: History chunk keyed by provider ID
Store->>Store: Reconcile history and live chunks

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_{Reviews (1): Last reviewed commit: "fix(agent-adapter): reconcile Claude mes..." | Re-trigger Greptile}