fix(server): opening a large database no longer blocks startup for minutes

[thymikee]

Problem

A 48 GB statev2.sqlite kept the backend from starting for minutes.

• Slow startup. Opening a database with no sqlite_stat1 ran PRAGMA optimize = 0x10012 (fix(server): collect SQLite planner statistics when the database opens #18471) before the server could answer. That pass reads every page of the large tables: 3 min 47 s on the 48 GB database. The service launcher's 30-minute prepared deadline and its docs name this pass as one of the costs.
• Check for Updates opened the window too early. Clicking it during that startup opened the main window before the backend was ready, leaving the renderer on a failed auth bootstrap.

Change

• Fixed planner statistics (persistence/plannerStatistics.ts). After migrations, the server adds sqlite_stat1 rows for indexes that have none, then loads them with ANALYZE sqlite_schema, which reads no user table.
  • The rows come from a full ANALYZE of the 48 GB database. Indexes on tables that were empty there get estimates.
  • Rows a database already has, including ones optimize collected, are kept.
  • The planner mostly needs each index's relative selectivity, so fixed rows give a new database and a 50 GB one the same plans.
  • A test fails when a migration adds an index without a row here, or when a row names an index that no longer exists.
• Desktop menu (DesktopApplicationMenu.ts). Check for Updates now uses activate instead of ensureMain. This brings back the connecting splash while the backend is down and opens the main window only once it is ready. The update result dialogs never needed the main window. This was the only caller outside DesktopWindow that could open the window before the backend was ready.

Scope and approval

This is part of making database growth self-managing. Repeated node updates are now skipped by #19429, and #19451 deletes superseded snapshots. This PR takes the size-dependent statistics pass off the startup path. It refines #18471 rather than reverting it: databases still get statistics, just without the table scan.

Verification

All measurements were taken on a copy of a real 47.9 GB database (13.9M events), using copy-on-write clones with sqlite_stat1 removed, on Node 26 / SQLite 3.53.4 (the same SQLite as Electron 44).

• Startup. The old setup PRAGMAs plus optimize took 226,581 ms. The new Sqlite.layerFromPath took 21 ms and left 148 rows in sqlite_stat1. A full ANALYZE, for reference, took 3 min 02 s.
• Query plans. I ran EXPLAIN QUERY PLAN on the 249 static server statements that prepare, under three conditions: no statistics, statistics from optimize, and the seeded rows.
  • No statistics changes 6 plans. The worst is ThreadFind, which then walks orchestration_events by application_event_version, a column with two values (half of 14M rows), instead of by stream_id.
  • The seeded rows pick the stream index there too.
  • The seeded rows differ from the optimize statistics in 10 plans. Each still uses an index of similar selectivity, except on tables of a few rows, where a scan is cheaper.
  • The runtime recovery reads from [Bug]: Server never collects SQLite planner statistics, so large databases full-scan and stop answering #17955 use their recovery indexes under all three conditions.
• Tests. vp test run passes on Sqlite.test.ts, serviceLauncher.test.ts and DesktopApplicationMenu.test.ts. Typecheck passes for server and desktop, and lint and format pass on the changed files.
• Not checked. I did not click Check for Updates in a packaged desktop build during a slow startup. The change only reroutes the click through the existing activate path.

Made by Claude Opus 5.5 in Claude Code, working in T3 Code.

🤖 Generated with Claude Code

[chatgpt-codex-connector]

Codex Review Summary

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Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-10-14T12:04:03.824721Z	cac318d	PR opened

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[macroscopeapp]

Approvability

Verdict: Not approved

Macroscope's review found this PR not approvable — The PR makes broad production-path changes: it replaces SQLite's startup statistics collection with fixed planner data, changes which streaming events are persisted, and alters desktop startup activation. The intent and tests are clear, but the cross-cutting runtime and durable-data effects merit human review.

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Reviewing files that changed from the base of the PR and between d061634 and 8f376f9.

📒 Files selected for processing: 1

• apps/server/src/persistence/plannerStatistics.ts

🚧 Files skipped from review as they are similar to previous changes: 1

• apps/server/src/persistence/plannerStatistics.ts

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📝 Walkthrough

The update-menu handler now activates the existing desktop window before checking for updates. SQLite persistence setup seeds configured planner statistics after migrations, and tests check statistics coverage and preservation of existing values.

Changes: Desktop update menu

Layer / File(s)	Summary
Activate the existing window apps/desktop/src/window/DesktopApplicationMenu.ts	The update-menu handler activates the existing desktop window before checking for updates, instead of ensuring the main window.

SQLite planner statistics

Layer / File(s)	Summary
Define planner estimates apps/server/src/persistence/plannerStatistics.ts	A readonly map associates known index names with fixed sqlite_stat1 statistic strings.
Seed and verify planner statistics apps/server/src/persistence/Sqlite.ts, apps/server/src/persistence/Sqlite.test.ts, apps/server/src/persistence/plannerStatistics.ts, apps/server/src/serviceLauncher.ts, docs/internals/server-updates.md	SQLite setup seeds mapped statistics for indexes without existing statistics after migrations. Tests check index coverage and preservation of existing values. Timeout comments and documentation no longer identify open-time optimization as preparation work.

Priority: ➖ Normal

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

Change: Bug fix

Sequence Diagram(s)

sequenceDiagram
  participant SqliteSetup
  participant Migrations
  participant seedPlannerStatistics
  participant sqlite_stat1
  SqliteSetup->>Migrations: Run migrations
  SqliteSetup->>seedPlannerStatistics: Seed planner statistics
  seedPlannerStatistics->>sqlite_stat1: Find indexes without statistics
  seedPlannerStatistics->>sqlite_stat1: Insert mapped statistics and reload

Loading

Merge Risk: ⚪ Minimal · up to 8f376

The change speeds up opening large databases that lack planner statistics and makes Check for Updates activate the existing window. No actionable merge-blocking risk remains.

Security architecture risk: 🔵 Low · up to cac31

The inspected changes preserve event ownership checks and separate approval controls, while limiting database writes to planner metadata. No introduced security vulnerability was established. Concurrent initialization, interrupted startup and downgrade behavior remain unverified.

Retained concerns
No architecture-level concerns identified.

Security review details

Security Blast Radius

• inferred — Planner effects span indexed tables in each opened application database, including authentication/session indexes. Deduplication affects event persistence within a run subscription and its routed child threads. Neither inspected change adds a new caller authority or credential capability.

Trust Boundaries and Controls

• observed — Approval and user-input authority updates use the separate runtime_request.updated event path. The new node-snapshot deduplication does not handle that event type, and node waiting, completed, interrupted, failed, cancelled and rolled-back states remain deliverable.

Resilience and Maintainability Implications

• observed — The cache advances before ingestion, but an ingestion error terminates the stream drain rather than continuing to consume duplicates against that cache. The failure path attempts ownership-gated run finalization and ensures subscription closure. Cache state is local to the execution subscription rather than durable across recovery.

Pre-merge checks: 4

Passed checks: 4 passed

Check name	Status	Explanation
Title check		The title clearly and concisely describes the primary server startup fix for large databases. It also matches the reported change scope.
Description check		The description is complete and relevant. It explains the problem, implementation, scope, performance results, query-plan checks, tests, and the untested packaged-desktop scenario. The scope section d…
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

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Actionable comments posted: 1

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Inline comments:
Review comments at @apps/server/src/persistence/plannerStatistics.ts:
- Around line 178-187: Update seedPlannerStatistics to run the initial ANALYZE,
missing-index selection, optional INSERT, and final ANALYZE inside one SQL
transaction using the client’s transaction API, so the write lock is acquired
before selection and concurrent initializations cannot seed the same indexes.

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📥 Commits

Reviewing files that changed from the base of the PR and between 8e018ff and cac318d.

📒 Files selected for processing: 8

• apps/desktop/src/window/DesktopApplicationMenu.ts
• apps/server/src/orchestration-v2/assistantStreaming.test.ts
• apps/server/src/orchestration-v2/assistantStreaming.ts
• apps/server/src/persistence/Sqlite.test.ts
• apps/server/src/persistence/Sqlite.ts
• apps/server/src/persistence/plannerStatistics.ts
• apps/server/src/serviceLauncher.ts
• docs/internals/server-updates.md

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Reviewed commit: cac318d6ce

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[t3dotgg]

Note

🤖 Claude Opus 5.5 responding on behalf of Theo

The repeated-node part of this PR is now on main. #19429 skips any node.updated that matches the stored node, in ProviderEventIngestor. It compares with the stored row instead of the last update the run sent, because the server also writes nodes, for example when a user answers an approval.

#19429 does not cover the planner statistics or the desktop menu fix. Please remove the assistantStreaming.ts change and rebase.

[thymikee]

Note

🤖 Claude Opus 5.5 responding on behalf of Michał

Done in d061634. The assistantStreaming.ts change is gone and the branch is rebased onto main with #19429. The PR now holds only the planner statistics and the desktop menu fix, and the description is updated to match.

[juliusmarminge]

Note

Grok responding on behalf of Julius.

Superseded by #21122, which continued this work with your commits and authorship kept (including the Check for Updates menu fix) and just merged. Thanks @thymikee!

[thymikee]

Thank you!