fix(codex): launch-arg MCP servers survive the thread's t3-code server

[lnieuwenhuis]

Fixes #15828

Codex thread config sent mcp_servers: { "t3-code": ... }. Codex applies per-thread config in the same layer as the process's -c flags, so that single-segment key replaced the whole mcp_servers table, and servers added through instance launch args (-c mcp_servers.extra.command=...) never started.

The thread config now uses the dotted key "mcp_servers.t3-code", the same way CODEX_THREAD_CONFIG already sets tools.update_plan.enabled. It's built in one place, codexThreadRuntimeParams, which covers thread/start, thread/resume and thread/fork. The replay matcher in effect-codex-app-server drops mcp_servers.* keys as well as the whole-table key, so recordings keep ignoring the per-machine URL and auth header.

Verification

• Probed a real codex app-server (codex-cli 0.160.0, isolated CODEX_HOME) launched with -c mcp_servers.extra.command="cat", then sent thread/start with each config shape and collected mcpServer/startupStatus/updated notifications:
  • whole table (mcp_servers: { "t3-code": ... }): only t3-code starts
  • dotted key ("mcp_servers.t3-code": ...): both t3-code and extra start
• vp test run on CodexAdapterV2.test.ts (asserts the dotted key and that no mcp_servers table is sent), CodexReplayFixtures.integration.test.ts, and the ThreadFork / OrchestratorReplayRecovery / ThreadMergeBack integration tests: all pass.
• effect-codex-app-server typecheck clean. t3 typecheck is clean apart from the duplicate Option import on main, fixed separately in fix(server): the server starts again after a duplicate Option import #15837.

Model/harness: Claude Opus 5.5 / Claude Code.

[macroscopeapp]

Approvability

Verdict: Approved at 157d583

Macroscope's review found this PR approvable — This is a small, localized Codex bug fix that preserves launch-argument MCP servers while still injecting the T3 server, with no schema, deployment, product-default, or static-analysis changes. The replay adjustment and updated unit expectation are correspondingly narrow.

No code changes detected at 39dd5d4. Prior analysis still applies.

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Reviewing files that changed from the base of the PR and between ad5178a and 157d583.

📒 Files selected for processing (3)

• apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts
• apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts
• packages/effect-codex-app-server/src/replay.ts

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📝 Walkthrough

Walkthrough

The Codex thread runtime configuration now uses a dotted key for the t3-code MCP server. Thread request normalization excludes mcp_servers and keys prefixed with mcp_servers.. The adapter test fixture uses the dotted key.

Changes

Codex MCP configuration override

Layer / File(s)	Summary
Configure and normalize thread MCP servers apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts, packages/effect-codex-app-server/src/replay.ts, apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts	The thread runtime config sets t3-code under mcp_servers.t3-code, preserving its URL and Authorization header. Request normalization filters mcp_servers and all mcp_servers.* keys. The test fixture uses the dotted key.

Priority: ➖ Normal

Estimated code review effort: 2 (Simple) | ~8 minutes

Change: Bug fix · Severity of issue fixed: Medium

Suggested reviewers: juliusmarminge

Merge Risk: ⚪ Minimal · up to 157d5

The configuration change is mergeable; no actionable current-head risk was established.

Architecture Summary

Architecture risk: 🔵 Low · up to 157d5

The change affects 2 systems.

Changed systems: apps/server, packages/effect-codex-app-server

Architecture concerns
No architecture-level concerns identified.

Review details

Systems and components

• observed — apps/server (service) was modified; 2 changed files map to changed impact.
• observed — packages/effect-codex-app-server (library) was modified; 1 changed file maps to changed impact.

Before / after behavior

• observed — Modified behavior in apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts: The test fixture changes the MCP server config from a nested mcp_servers object to the flattened mcp_servers.t3-code key, preserving the endpoint and Authorization header.
• observed — Modified behavior in apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts: The MCP server configuration changes from a nested mcp_servers table to the dotted mcp_servers.t3-code key; its URL and authorization header remain the same.
• observed — Modified behavior in packages/effect-codex-app-server/src/replay.ts: Thread request normalization now filters out mcp_servers and all mcp_servers.* config keys; previously it removed only the exact mcp_servers key.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 2 functions across 3 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title identifies the main change: preserving MCP servers configured through launch arguments when the thread adds the t3-code server.
Description check	✅ Passed	The description explains the problem, the fix, and the verification results. It links issue #15828, but does not explicitly state maintainer approval or explain why the fix qualifies as a small, obvio…
Linked Issues check	✅ Passed	Issue #15828 requires Codex threads to retain MCP servers configured with instance -c flags while adding T3’s t3-code server. codexThreadRuntimeParams now sends mcp_servers.t3-code instead of …
Out of Scope Changes check	✅ Passed	All changes relate to issue #15828. The replay matcher now ignores both whole-table and dotted mcp_servers config keys, so per-machine MCP settings do not cause replay request mismatches. The adapte…

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