App Server init/proxy failure blocks programmatic archival fallback

Summary

A Codex automation session completed repository cleanup but could not archive its own completed thread through the documented thread/archive RPC. The automation tool surface did not expose thread/archive, so it attempted the local App Server fallback. That path failed before the archive operation could be called.

This issue tracks the fallback-path failure and diagnostics. The direct feature request to expose current-thread archival is tracked separately in #44784.

Environment

• codex-cli 0.152.0
• Linux 4.4.302+ x86_64
• Hosted/containerized Codex automation environment
• No raw session JSONL, credentials, thread IDs, or local paths are included

Initial reproduction

1. Complete a Codex automation task and clean up its Git worktree.
2. Attempt to archive the completed thread through the documented App Server API.
3. Initialize a separate App Server and call thread/list to obtain the current thread ID.

Sanitized request:

printf '%s\n' \
  '{"method":"initialize","id":1,"params":{"clientInfo":{"name":"cleanup-audit","title":"Cleanup audit","version":"1.0"}}}' \
  '{"method":"initialized"}' \
  '{"method":"thread/list","id":2,"params":{"limit":100}}' |
  codex app-server --stdio

Observed result:

Error: failed to initialize sqlite state runtime under $CODEX_HOME: failed to initialize state runtime at $CODEX_HOME

Follow-up diagnostics

• codex doctor --summary reported the SQLite state databases as healthy.
• It reported three thread-index inconsistencies: rollout files missing from the state DB or rows pointing to missing/unusable rollout files.
• A persistent App Server was already running.
• The separate codex app-server --stdio failure therefore did not establish database corruption or a root cause.
• codex app-server proxy against the persistent daemon completed without an RPC response, so the automation still could not obtain the current thread ID or call thread/archive.

Expected behavior

The App Server fallback should either:

• initialize and expose the underlying state correctly;
• provide an actionable diagnostic and safe recovery path; or
• provide a supported bridge to the persistent App Server instance.

Impact

When direct current-thread archival is unavailable, the documented App Server fallback is also unusable. Repository cleanup can complete while session cleanup remains a manual UI action.

Related

• #44784 tracks the direct, narrowly scoped enablement request.
• #30105 covers a similar generic App Server SQLite initialization symptom caused by concurrent access on macOS; this report does not assume the same root cause.
• #39130 covers a Windows archive file-move failure after an archive attempt; this report fails before thread/archive can run.

Start by reproducing the failure with codex app-server --stdio, then compare its initialization path with codex app-server proxy and the results of codex doctor --summary. Done means the fallback initializes successfully, reports an actionable diagnostic and safe recovery path, or provides a supported bridge to the persistent App Server.