## What changed
- Add `SqliteConfig` to own the resolved SQLite home, runtime database paths,
and shared read/write and read-only pool settings.
- Pass the configuration through state and local thread-store consumers,
replacing standalone path helpers and duplicated connection setup.
GitOrigin-RevId: 7351b08da94b5c8b6c0bbe492f86aeeca0699d3c
## Why
`SqliteConfig` stores its home as an `AbsolutePathBuf`, but its test constructor
previously accepted a `PathBuf` and checked the absolute-path invariant at
runtime.
## What changed
- Make `SqliteConfig::new_for_testing` accept an `AbsolutePathBuf` directly,
removing its fallible conversion and `expect`.
- Update SQLite test setup to convert temporary directory paths with
`PathExt::abs` at each call site.
GitOrigin-RevId: 93585b9aea805e2449b3465ac20eeb39417ed555
## Why
The thread inventory check compared state database rows only with plain
`.jsonl` rollout files. Once a rollout was compressed to `.jsonl.zst`, the
check could report its canonical database row as stale and omit the rollout
from parity results.
## What changed
- Scan completed compressed rollouts and match them to database rows using
their canonical `.jsonl` paths.
- Prefer a plain rollout when both plain and compressed siblings exist, and
ignore compression temporary files.
- Keep unreadable compressed rollouts in the set of existing paths so they
produce scan errors without also producing misleading stale-row reports.
- Use canonical paths when deriving legacy thread IDs and archived status.
## Testing
Added coverage for active and archived compressed rollouts, plain/compressed
siblings, metadata and legacy filename IDs, corrupt compressed data, and
compression temporary files.
GitOrigin-RevId: 2461376432194a4062beedbe875aa7002dd2049f
## 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
Callers that only need session metadata should not scan an entire rollout or fail on an unreadable tail after valid metadata.
## What changed
- Read session metadata directly from the rollout line reader, stopping as soon as it is found for both plain and compressed rollouts while preserving pre-header and validation behavior.
- Bound the doctor thread inventory scan to the first 64 non-empty header lines. Prefer the metadata thread ID and retain the validated filename fallback for legacy rollouts without metadata.
## Testing
- Cover invalid UTF-8 tails, compressed rollouts, pre-header records, metadata and filename ID mismatches, the scan boundary, legacy fallback, and unusable headers.
GitOrigin-RevId: 49576bd2877942e64082ce5ed057ecc848c025ec
## Why
Paginated thread history needs durable ordering so consumers can process a rollout suffix without rebuilding all earlier history.
## What changed
- Add optional, zero-based ordinals to `RolloutLine` records in paginated rollouts while leaving legacy rollout serialization unchanged.
- Continue ordinals from the last valid record when appending or resuming, including after gaps or an incomplete tail, and reject overflow without appending.
- Add a stateless `project_rollout_line` helper that maps canonical turn lifecycle and completed-item records into thread-history change sets.
## Testing
- Cover ordinal assignment, legacy compatibility, resume and tail recovery, overflow handling, and thread-history projection for completed, failed, and interrupted turns.
GitOrigin-RevId: 3a9bb6cd2a1f674a9f154342e96e9aa3d8330781
## Summary
A cold-resumed subagent kept its durable thread ID but could receive a
new session ID, splitting one agent tree across multiple sessions after
a restart.
Persist the root session ID in every rollout `SessionMeta`, carry it
through thread creation, and restore it before initializing the resumed
`Session` and `AgentControl`.
## Behavior
For a nested agent tree:
```text
root session R
parent thread P
child thread C
```
The child rollout stores:
```text
session_id: R
parent_thread_id: P
id: C
```
After a cold resume, the child still belongs to root session `R` while
its immediate parent remains `P`. The integration coverage uses distinct
values for all three IDs so it catches restoring the session from
`parent_thread_id`.
## Legacy rollouts
Previous rollouts have `id` but no `session_id`. `SessionMetaLine`
deserialization treats a missing `session_id` as `id`, keeping those
files readable, listable, and resumable. When a legacy subagent is
resumed through its root, that synthesized child ID no longer overrides
the inherited root-scoped `AgentControl`. New rollouts always persist
the explicit root session ID.
## 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
```
Adam Perry @ OpenAI