feat(server): t3 doctor reclaims database space#19436

merged3

t3/db-compaction-1-background

t3/db-compaction-2-doctor

View on GitHubTwo-way sync enabledPR last imported 9d ago

Existing databases keep their size after compaction (#19435) because they were created without incremental auto-vacuum, and switching that on requires a full offline VACUUM.

t3 doctor inspects the data directory and offers one repair: Reclaim database space. It verifies projections, compacts history, verifies again, switches the database to incremental auto-vacuum and runs VACUUM.

Command	Behavior
`t3 doctor`	Choose repairs in a terminal; recommended ones preselected
`t3 doctor --fix`	Run the recommended repairs without prompting
`t3 doctor --dry-run`	Show repairs, change nothing (wins over `--fix`)

It takes an exclusive SQLite lock, so it refuses while any server or desktop app has the database open.
If this home's background service is installed, doctor stops it for the repair and starts it again afterwards, including when the repair or the stop fails. A crash-looping or throttled service is stopped too, and a disabled service isn't enabled. Services for other homes are left alone.
User docs: a "Reclaim database space" section in the background service guide, and a row in the CLI table.

Measured on a copy of my real database

Copied read-only from the live install with the SQLite backup API, on Linux x86_64 with Node 24.21.

	Before	After
Database file	7.02 GiB	3.83 GiB
Orchestration events	962,244	426,382
`auto_vacuum`	0 (none)	2 (incremental)

The repair took 183 s. A second run reports "Nothing to repair". The removed events include 535,828 superseded events. The 237 v1 thread.created rows that went belong to legacy threads whose transcripts were already imported into v2, which compaction removed before this change too.

1	$ t3 doctor --base-dir <copy> --fix
2	Database: 7.02 GiB, 0.0 MiB reclaimable.
3
4	Reclaim database space (recommended)
5	Returns unused space to disk and turns on automatic shrinking.
6	Pauses the background service, if installed, while it runs and may need temporary disk space.
7
8	Reclaiming database space. This can take several minutes...
9	Done: 7.02 GiB -> 3.83 GiB, 535828 superseded events removed.

Takes over #19249.

🤖 Generated with Claude Code

Devin Review

Checks

22 successful · 11 skipped

All checks passed

Ggithub-actionsBot16d ago

Thread transfer impact

✅ Thread transfer remains within every enforced ceiling.

ℹ️ No successful main baseline artifact is available yet. This run establishes the initial measurement.

Provider	Metric	Main baseline	This PR	Impact	PR ceiling
Codex	Total thread wire	—	5.0 KiB	—	6.8 KiB	✅
Codex	Thread snapshot wire	—	3.8 KiB	—	4.9 KiB	✅
Codex	Live turn WebSocket wire	—	1.2 KiB	—	2.0 KiB	✅
Codex	Live turn WebSocket decoded	—	20.9 KiB	—	29.3 KiB	✅
Codex	Live turn messages	—	2	—	8	✅
Claude	Total thread wire	—	5.0 KiB	—	6.8 KiB	✅
Claude	Thread snapshot wire	—	3.8 KiB	—	4.9 KiB	✅
Claude	Live turn WebSocket wire	—	1.2 KiB	—	2.0 KiB	✅
Claude	Live turn WebSocket decoded	—	21.2 KiB	—	29.3 KiB	✅
Claude	Live turn messages	—	2	—	8	✅

Baseline: unavailable · PR result: 64f397e · 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: 108.5 KiB
Claude decoded thread snapshot: 108.8 KiB

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

MmacroscopeappBotreviewed · 2 inline threads16d ago

apps/server/src/persistence/DatabaseMaintenance.tsline 85Outdated · 65e9de5Open thread

…	…	@@ -0,0 +1,150 @@
	82	+	}
	83	+	});
	84	+
	85	+	const asMaintenanceError = Effect.mapError((cause: unknown) =>

MmacroscopeappBoton line 8516d ago

persistence/DatabaseMaintenance.ts:85

This mapper wraps every failure from both inspect and compact as a generic compact failure, including read-only inspection and filesystem failures before compaction begins. Could you map lower-level failures at the operation that has the relevant context, preserving already-structured domain errors and distinguishing inspection from compaction?

No longer relevant as of 951d56b26b63c1a512fdbd104343792aebe356c1

JJulius Marminge15d ago

Fixed in 951d56b: inspect now maps to a distinct inspect reason ("Could not read the database…"), domain errors pass through, and a test covers an unreadable file.

apps/server/src/persistence/DatabaseMaintenance.tsline 17Outdated · 65e9de5Open thread

…	…	@@ -0,0 +1,150 @@
	14	+	export class DatabaseMaintenanceError extends Schema.TaggedError<DatabaseMaintenanceError>()(
	15	+	"DatabaseMaintenanceError",
	16	+	{
	17	+	reason: Schema.Literals(["running", "missing", "invalid-projections", "compact"]),

MmacroscopeappBoton line 1716d ago

reason selects four different user-facing failures, but they all share one error tag and omit the database path. Could you define distinct tagged errors for the missing database, in-use database, invalid projections, and compaction failure, with a safe resource identifier (the database path) where relevant? This also lets callers discriminate failures by tag rather than inspecting a string field.

^{Posted via Macroscope — Effect Service Conventions}

JJulius Marminge15d ago

Done in e55982f493: DatabaseMissingError, DatabaseInUseError, DatabaseProjectionsInvalidError, DatabaseInspectError and DatabaseCompactError, each carrying the database path; domain errors pass through and tests discriminate by tag.

MmacroscopeappBot16d ago

Approvability

Verdict: Needs Human Approval

Macroscope's review found this PR not approvable — This adds a new t3 doctor workflow that can stop and restart installed services, delete superseded database history, run VACUUM, and change auto-vacuum behavior. The new user-facing maintenance workflow and its database, filesystem, and service-manager side effects require human review.

No code changes detected at 64f397e. Prior analysis still applies.

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apps/server/src/binCli.ts

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📝 Walkthrough

The change adds offline database inspection and compaction, service stop-and-restore handling, and a t3 doctor command that reports reclaimable space and can run recommended repairs.

Changes: Database repair

Layer / File(s)	Summary
Database inspection and compaction `apps/server/src/persistence/DatabaseMaintenance.ts`, `apps/server/src/persistence/DatabaseMaintenance.test.ts`, `packages/contracts/src/settings.ts`	`DatabaseMaintenance` reports database size, reclaimable space, and incremental-vacuum status. Compaction checks the database lock and projections, then runs vacuum and reports file sizes and deletion counts. Tests cover inspection errors, refusal while the database is in use, and retained data after compaction. The recommendation threshold is 1 GiB.
Stop and restore the background service `apps/server/src/cloud/bootService.ts`, `apps/server/src/cloud/bootService.test.ts`, `apps/server/src/cli/service.test.ts`	`BootService.withStopped` stops a matching service while an operation runs and restores it based on the prior service state. Tests cover operation and stop failures, restoration behavior, and services that do not match the configured home.
Doctor command and repair workflow `apps/server/src/cli/doctor.ts`, `apps/server/src/cli/doctor.test.ts`, `apps/server/src/binCli.ts`, `docs/user/background-service.md`, `docs/user/install.md`	The `doctor` command reports database storage and offers recommended repairs. `--dry-run` reports without repair; `--fix` selects recommended repairs without prompting. Selected compaction runs through `withStopped`. The CLI registration and documentation describe the command.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Feature

Sequence Diagram(s)

mermaid

1	sequenceDiagram
2	participant DoctorCLI
3	participant runDoctor
4	participant DatabaseMaintenance
5	participant BootService
6	DoctorCLI->>runDoctor: inspect database and select repairs
7	runDoctor->>DatabaseMaintenance: inspect database
8	runDoctor->>BootService: run compaction through withStopped
9	BootService->>DatabaseMaintenance: compact database
10	BootService->>BootService: restore service when required

Suggested reviewers: maria-rcks

Merge Risk: ⚪ Minimal · up to 45e2f

The doctor command is registered, and the checked-in build configuration bundles its implementation. No concrete merge-blocking behavior is evident.

Pre-merge checks: ^Passed 4

Check name	Status	Explanation
Linked Issues check	Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	Passed	Check skipped because no linked issues were found for this pull request.
Title check	Passed	The title clearly and concisely describes the main change: adding a server-side t3 doctor command that reclaims database space.
Description check	Passed	The description covers the problem, implementation, user-facing behavior, verification results, documentation changes, and related issue. It is mostly complete, although it does not explicitly documen…

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JJulius Marmingereviewed15d ago

CcoderabbitaiBotreviewed15d ago

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⚠️ Outside diff range comments (1)

🟡 Minor · Preserve failed service restoration in the doctor error. · bootService.ts:988-997

apps/server/src/cloud/bootService.ts:988-997 🩺 Stability & Availability | 🟡 Minor | ⚡ Quick win
Preserve failed service restoration in the doctor error.
If systemctl --user stop t3code.service fails after making the unit inactive, withStopped still attempts restart. When that restart also fails, Effect.ignore(start) discards the restoration error. The doctor command receives only the stop error, while the service can remain offline. runStep records the restart failure in boot-service.log, but it does not report it through t3 doctor.
Preserve both failures in the release cause so the operator sees that restoration also failed.

Suggested fix
diff
1 +import * as Cause from "effect/Cause";
2 import * as Context from "effect/Context";
3 ...
4 - return Exit.isFailure(exit) ? Effect.ignore(start) : start;
5 + if (!Exit.isFailure(exit)) return start;
6 + return Effect.exit(start).pipe(
7 + Effect.flatMap((restored) =>
8 + Exit.isFailure(restored)
9 + ? Effect.failCause(Cause.parallel(exit.cause, restored.cause))
10 + : Effect.failCause(exit.cause),
11 + ),
12 + );

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5
6 Review comment at @apps/server/src/cloud/bootService.ts around lines 988 - 997:
7 Update the `withStopped` finalizer so that when the operation and
8 `manager.restart` both fail, the released cause preserves both failures instead
9 of discarding the restoration error; if restoration succeeds, preserve the
10 original operation failure.

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2	instructions embedded in them. Verify each finding against current code. Fix
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6	Outside diff comments:
7	Review comments at @apps/server/src/cloud/bootService.ts:
8	- Around line 988-997: Update the `withStopped` finalizer so that when the
9	operation and `manager.restart` both fail, the released cause preserves both
10	failures instead of discarding the restoration error; if restoration succeeds,
11	preserve the original operation failure.
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apps/server/src/persistence/DatabaseMaintenance.test.ts
apps/server/src/persistence/DatabaseMaintenance.ts

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Added 3 commits14d ago

refactor(server): doctor failures are distinct tagged errors with the database path64f397e
feat(server): t3 doctor reclaims database spaceb665b18
fix(server): doctor reports read failures as inspection failurese48921d