## Why
Diagnostic uploads skip the doctor attachment if report generation exceeds its
overall timeout. SQLite integrity scans can be delayed by large databases or
lock contention.
## What changed
- Give each database integrity scan a one-second deadline when collecting a
diagnostic attachment.
- Interrupt scans and lock waits at the deadline, preserve any corruption rows
already returned, and report an incomplete clean scan as a warning.
- Keep direct `codex doctor` integrity checks unbounded.
## Testing
- Cover interrupted scans, lock waits, retries without a deadline, and
corruption results returned before interruption.
GitOrigin-RevId: 4817fb459ac53953669a9ba5f03397a6fc82c72e
## Why
Codex and SQLite data can use separate home directories, but state consumers
could reconstruct database paths from the Codex home instead of consistently
using the resolved SQLite configuration.
## What changed
- Pass `SqliteConfig` through the core, rollout, state runtime, and thread store
instead of passing a directory and rebuilding the configuration downstream.
- Use that shared configuration for state, logs, memories, goals, and paginated
thread-history database access, including integrity checks and cleanup.
- Reject state database handles whose SQLite configuration does not match the
requesting store.
## Testing
Add coverage with separate Codex and SQLite homes that verifies startup
backfill, thread listing, and paginated history all use the configured SQLite
directory.
GitOrigin-RevId: 1de1cdd1d6ff1d70bbb6c360c8352e6543fb8ebf
## What changed
- Add `SqliteConfig` as the shared entry point for read-write and read-only SQLite pools.
- Apply consistent WAL, synchronization, auto-vacuum, busy-timeout, logging, and pool-size settings to writable Codex databases.
- Route state runtime, audit, CLI, and test database connections through the shared configuration.
## Testing
- Run migration tests against temporary on-disk databases opened through `SqliteConfig`, including the concurrent-writer repair case.
GitOrigin-RevId: e3946b98bde04c47574532ac8b1a7bb2b03edd97
## Why
Users have been reporting missing sessions in the app. The app server
thread listing is backed by the SQLite state DB, but the durable source
of truth for a thread still exists on disk as rollout JSONL. When the
state DB is incomplete, doctor should be able to show the mismatch
directly instead of leaving users with a generic state health result.
## What changed
This adds a `threads` doctor check that compares active and archived
rollout files under `CODEX_HOME` with rows in the SQLite `threads`
table. The check reports missing rollout rows, stale DB rows, archive
flag mismatches, duplicate rollout thread IDs, duplicate DB paths,
source/provider summaries, and bounded samples of affected rollout
paths.
It also adds a read-only state audit helper in `codex-rs/state` so
doctor can inspect thread rows without creating, migrating, or repairing
the database.
## Sample output
```text
⚠ threads rollout files are missing from the state DB
default model provider openai
rollout DB active files 3910
rollout DB archived files 2037
rollout DB scan errors 0
rollout DB malformed file names 0
rollout DB scan cap reached false
rollout DB rows 5499
rollout DB active rows 3462
rollout DB archived rows 2037
rollout DB missing active rows 448
rollout DB missing archived rows 0
rollout DB stale rows 0
rollout DB archive mismatches 0
rollout DB duplicate rollout thread ids 0
rollout DB duplicate DB paths 0
rollout DB model providers openai=5359, lmstudio=35, mock_provider=33, lite_llm=26, proxy=26, ollama=15, lms=4, local-usage-limit=1
rollout DB sources vscode=2587, cli=1494, subagent:thread_spawn=577, subagent:other=502, exec=281, subagent:memory_consolidation=46, subagent:review=9, unknown=3
rollout DB missing active sample ~/.codex/sessions/2026/0…857e-a923c712e066.jsonl
rollout DB missing active sample ~/.codex/sessions/2025/0…877a-766dff25c68d.jsonl
rollout DB missing active sample ~/.codex/sessions/2025/0…a8b1-7bbadc836f6e.jsonl
rollout DB missing active sample ~/.codex/sessions/2025/0…a218-e6197f3f62f8.jsonl
rollout DB missing active sample ~/.codex/sessions/2025/0…9011-7e30784f9932.jsonl
```
chess