perf(server): cap SQLite WAL size after checkpoints

[t3dotgg]

Requested by Theo · project thread

What Changed

Sqlite.ts now sets PRAGMA journal_size_limit = 16777216. When a checkpoint resets the WAL, SQLite now truncates the file back to 16 MiB. Before this change, the WAL stayed at its peak size forever. Existing bloated WALs shrink at their next checkpoint reset, so no migration is needed.

The replay-guard file sweep that was first in this PR has been removed, because #13695 already covers it.

Why

A user perf report showed on-disk state that only grows. The WAL grows to its largest-ever size, for example after a big write burst or while a long read holds off checkpoints, and never shrinks back. The server uses one connection, so a single pragma in the shared setup covers it.

Checklist

• This PR is small and focused
• I explained what changed and why
• No UI changes

The new test writes 24 MiB, then makes a few more writes that cross the autocheckpoint threshold, and checks that the WAL is at most 16 MiB. Without the pragma the test fails with the WAL still at 25.7 MB. With the pragma it passes. tsc --noEmit for apps/server is clean.

Model and harness: Claude Opus 5.5 via Claude Code.

🤖 Generated with Claude Code

https://claude.ai/code/session_01Y1jWssjvT14xf2uw1daK7Z

[github-actions]

Thread transfer impact

✅ Thread transfer remains within every enforced ceiling.

Provider	Metric	Main baseline	This PR	Impact	PR ceiling
Codex	Total thread wire	13.5 KiB	13.5 KiB	−15 B (−0.1%)	15.1 KiB	✅
Codex	Thread snapshot wire	7.1 KiB	7.1 KiB	−4 B (−0.1%)	7.3 KiB	✅
Codex	Live turn WebSocket wire	6.4 KiB	6.4 KiB	−11 B (−0.2%)	7.8 KiB	✅
Codex	Live turn WebSocket decoded	56.2 KiB	56.2 KiB	0 B (0.0%)	66.4 KiB	✅
Codex	Live turn messages	9	9	0 (0.0%)	21	✅
Claude	Total thread wire	13.5 KiB	13.5 KiB	−9 B (−0.1%)	15.1 KiB	✅
Claude	Thread snapshot wire	7.1 KiB	7.1 KiB	−10 B (−0.1%)	7.3 KiB	✅
Claude	Live turn WebSocket wire	6.4 KiB	6.4 KiB	+1 B (+0.0%)	7.8 KiB	✅
Claude	Live turn WebSocket decoded	57.0 KiB	57.0 KiB	0 B (0.0%)	66.4 KiB	✅
Claude	Live turn messages	9	9	0 (0.0%)	21	✅

Baseline: ed809f7 · PR result: d9d6ab5 · Source CI: success

Scenario and decoded snapshot size

10 historical turns, 5 command tools per turn, 878.9 KiB retained MCP result per historical turn, and a 1.05 MiB retained result in the measured turn.

• Codex decoded thread snapshot: 114.0 KiB
• Claude decoded thread snapshot: 114.7 KiB

Updated in place by a trusted workflow. PR artifacts are strictly validated and never executed.

[macroscopeapp]

Approvability

Verdict: Not approved

Macroscope's review found this PR not approvable — The PR changes the default SQLite persistence behavior by enforcing a 16 MiB WAL size limit after checkpoints across existing deployments. The implementation is small and tested, but this product-default change requires human review.

Notes:

• No code objects were reviewed. Approvability was decided on eligibility alone.

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📝 Walkthrough

Walkthrough

The server now removes replay-guard files older than one hour on a recurring schedule. SQLite now sets a 16 MiB journal size limit. Tests cover replay-guard retention and WAL size.

Changes

Replay-Guard Pruning

Layer / File(s)	Summary
Scheduled replay-guard pruning apps/server/src/auth/ServerSecretStore.ts, apps/server/src/auth/ServerSecretStore.test.ts	pruneReplayGuards removes matching DPoP and cloud-proof markers older than one hour. The service runs pruning immediately and every 10 minutes, and logs pruning failures. The test checks that old markers are removed while a fresh marker and a session-signing key remain.

SQLite WAL Size Limit

Layer / File(s)	Summary
WAL journal size limit apps/server/src/persistence/Layers/Sqlite.ts, apps/server/src/persistence/Layers/Sqlite.test.ts	SQLite sets journal_size_limit to 16 MiB. The test checks that the WAL grows beyond 16 MiB after bulk writes and is at most 16 MiB after subsequent writes.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~20 minutes

Change: Bug fix · Severity of issue fixed: Medium

Suggested reviewers: juliusmarminge

Merge Risk: 🔵 Low · up to d9d6a

Pruning of replay markers and the WAL size limit are sound. A persistent filesystem error on one marker file would be skipped silently, so that file could remain without any warning. This is a minor follow-up, and the change is otherwise safe to merge.

🚥 Pre-merge checks | ✅ 2 | ❌ 3

❌ Failed checks (3 warnings)

Check name	Status	Explanation	Resolution
Linked Issues check	⚠️ Warning	For #9040, the PR adds bounded retention for matching DPoP and cloud replay-marker files. pruneReplayGuards removes matching files older than one hour, runs at service startup, and repeats every 10 …	Before accepting #9040, validate the bootstrap credential before verifyRequestDpopProof records replay state, and add an automated test for an invalid bootstrap credential that verifies no replay marker is created. Add or retain tests tha…
Out of Scope Changes check	⚠️ Warning	The SQLite changes set PRAGMA journal_size_limit to 16 MiB and add WAL-size tests. Direct issue #9040 concerns DPoP replay markers, replay retention, atomicity, and bootstrap-credential validation. …	Remove the SQLite pragma and WAL test from this pull request, or link the SQLite work to a directly relevant issue and submit it separately.
Description check	⚠️ Warning	The description includes the required What Changed, Why, and checklist sections, but it incorrectly states that replay-guard pruning was removed. The changeset still adds replay-guard pruning and rela…	Update the description to document the replay-guard pruning behavior, tests, and bounded-category warning logging. Remove the statement that this functionality was removed, or remove the corresponding code changes.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 4…
Title check	✅ Passed	The title clearly and concisely describes the SQLite WAL size change, which is a primary change in the pull request.

Full details: Linked Issues check

Explanation

For #9040, the PR adds bounded retention for matching DPoP and cloud replay-marker files. pruneReplayGuards removes matching files older than one hour, runs at service startup, and repeats every 10 minutes. The test verifies that old marker files are removed and session secrets remain. However, the PR does not change replay-marker write ordering or add a bootstrap-credential preflight. In auth/http.ts, the token handler calls verifyRequestDpopProof before exchangeBootstrapCredentialForAccessToken; this leaves the issue's invalid-bootstrap path able to record replay state before credential rejection. The PR also does not establish a change to the issue's atomic replay-state requirement.

Resolution

Before accepting #9040, validate the bootstrap credential before verifyRequestDpopProof records replay state, and add an automated test for an invalid bootstrap credential that verifies no replay marker is created. Add or retain tests that prove replay-marker writes remain atomic.

Full details: Out of Scope Changes check

Explanation

The SQLite changes set PRAGMA journal_size_limit to 16 MiB and add WAL-size tests. Direct issue #9040 concerns DPoP replay markers, replay retention, atomicity, and bootstrap-credential validation. The SQLite changes have no demonstrated connection to those requirements.

Full details: Description check

Explanation

The description includes the required What Changed, Why, and checklist sections, but it incorrectly states that replay-guard pruning was removed. The changeset still adds replay-guard pruning and related tests.

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Actionable comments posted: 1

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Inline comments:
In `@apps/server/src/auth/ServerSecretStore.ts`:
- Line 179: Update the per-file pruning flow in ServerSecretStore to replace
Effect.ignore with handling that continues to suppress disappearance races but
logs a bounded error category for other stat or remove failures, then continues
the sweep.

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ℹ️ Review info

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📥 Commits

Reviewing files that changed from the base of the PR and between ed809f7 and a929298.

📒 Files selected for processing (4)

• apps/server/src/auth/ServerSecretStore.test.ts
• apps/server/src/auth/ServerSecretStore.ts
• apps/server/src/persistence/Layers/Sqlite.test.ts
• apps/server/src/persistence/Layers/Sqlite.ts

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[juliusmarminge]

Superseded by #13684 (merged on main as 8aa5be2). Same fix: PRAGMA journal_size_limit in shared Sqlite setup so the -wal file shrinks after a checkpoint reset. #13684 uses 32 MiB; this PR's remaining diff is only the 16 MiB variant + test (replay-guard sweep already dropped for #13695).