Fix Private Lima Codex policy introspection

[toku345]

Summary

• sequence the Codex app-server initialize and policy-read requests by waiting for each response
• validate list-valued effective config through complete, uniform indexed origin metadata
• add fail-closed regression coverage and document the live C00 contract
• refresh the Private Lima harness manifest

Root cause

Codex 0.144.5 requires a stateful initialize handshake, but the validator sent the complete JSONL request stream before reading responses. In addition, list-valued config origins are reported per index (for example, writable_roots.0) while the normalizer only accepted a parent origin key.

Impact

The C00 runtime-policy validator can now inspect the pinned Codex guest without a false block while preserving fail-closed behavior for missing or mixed provenance.

Validation

• PYTHONDONTWRITEBYTECODE=1 python3 -W error::ResourceWarning -m unittest discover -s tests/outer_loop_lima -p 'test_*.py' — 148 tests passed, 1 skipped
• guest ShellCheck — passed
• strict harness manifest validation — passed
• git diff --check and bytecode absence checks — passed
• Lima 2.2.0 static validation for both week0 profiles — passed (sandbox-only Rosetta detection warning)
• retained Codex VM candidate validation — CANDIDATE_CODEX_POLICY_PASS (non-authoritative, candidate module loaded from guest /tmp)

[greptile-apps]

Greptile Summary

The PR repairs Codex runtime-policy introspection while retaining fail-closed provenance validation.

• Sequences initialization and policy-read requests against the stateful app-server protocol.
• Normalizes list-valued configuration using complete per-index origin metadata.
• Adds regression coverage, updates the documented C00 contract, and refreshes integrity hashes.

Confidence Score: 5/5

The PR appears safe to merge, with no concrete blocking or independently actionable non-blocking issues identified.

The interactive request lifecycle matches the documented stateful protocol, list provenance is checked uniformly per index, and failure paths remain fail-closed.

Important Files Changed

Filename	Overview
tools/outer-loop-lima-calibration/runtime/codex.py	Implements deadline-bound, sequential JSONL communication and fail-closed indexed-origin normalization without an identified defect.
tests/outer_loop_lima/test_runtime_policy.py	Adds handshake-order and indexed-provenance regression coverage, including missing and mixed-origin rejection.
tools/outer-loop-lima-calibration/manifest.json	Refreshes the hashes for the modified runtime module and README.
tools/outer-loop-lima-calibration/README.md	Documents request sequencing and the complete indexed-origin requirement.
docs/design/codex-claude-outer-loop-private-lima-calibration-implementation.md	Updates the design contract to describe stateful reads and fail-closed list provenance.

Sequence Diagram

sequenceDiagram
    participant V as C00 Validator
    participant C as Codex app-server
    V->>C: initialize (id 1)
    C-->>V: initialize result
    V->>C: initialized notification
    V->>C: config/read (id 2)
    C-->>V: config result with indexed origins
    V->>C: configRequirements/read (id 3)
    C-->>V: requirements result
    V->>V: Compare effective values and provenance

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_{Reviews (1): Last reviewed commit: "Handle buffered Codex app-server JSONL" | Re-trigger Greptile}