VACUUM snapshot metadata through the sqlite driver, not a CLI (closes #120)

snapshot create vacuumed the exported metadata database by shelling out
to a sqlite3 binary, so a backup failed at the very end on any host
without that CLI. vacuumDatabase now opens the database with the
modernc.org/sqlite driver and runs VACUUM through it, outside any
transaction; internal/snapshot no longer imports os/exec. The database
opens in WAL mode, so the close after VACUUM checkpoints the rewrite
into the main file that is compressed and uploaded. A new test deletes
marked rows, vacuums, and asserts the file shrank and no longer holds
the deleted bytes. script/bootstrap and the Dockerfile test image stop
installing the CLI.

Disclosure: the Dockerfile test-image change was not exercised by local
make check, which builds only the lint image.

Model: opus-4-8

Dockerfile

@@ -22,8 +22,10 @@ FROM golang:1.26.1-alpine@sha256:2389ebfa5b7f43eeafbd6be0c3700cc46690ef842ad962f
 
 ARG VERSION=dev
 
-# Install build dependencies for CGO (mattn/go-sqlite3) and sqlite3 CLI (tests)
+# Build tooling: make, plus a C toolchain because `go test -race` needs cgo.
-RUN apk add --no-cache make build-base sqlite
+# The sqlite driver is pure Go (modernc.org/sqlite), so no sqlite library or
+# CLI is required.
+RUN apk add --no-cache make build-base
 
 WORKDIR /src
 

README.md

@@ -603,7 +603,6 @@ regardless of color setting (emoji are not color).
   and the pre-commit hook both run it. A `golangci-lint` installed on
   `PATH` is not a substitute and is never used on a host, whatever its
   version.
-* `sqlite3` CLI, which the test suite shells out to
 * S3-compatible object storage (or local filesystem, or rclone remote)
 
 ## development workflow
@@ -634,8 +633,8 @@ standard: normalized scripts in `script/` are the entrypoints for the
 development workflow, and the Makefile targets are thin shims that call
 them. We provide:
 
-* `script/bootstrap` — install all development dependencies (go, sqlite3,
+* `script/bootstrap` — install all development dependencies (go, Go
-  Go module download). It deliberately does not install `golangci-lint`;
+  module download). It deliberately does not install `golangci-lint`;
   see `script/lint` below.
 * `script/setup` — make a fresh clone ready for development: runs
   `script/bootstrap`, then `script/install-precommit`

TODO.md

@@ -25,6 +25,14 @@ release" is exactly the contradiction
 
 # Completed Steps
 
+- 2026-09-21: Made `snapshot create` VACUUM the per-snapshot metadata
+  database through the `modernc.org/sqlite` driver instead of shelling
+  out to the external `sqlite` command-line binary (issue #120). A
+  backup no longer needs that binary on `PATH`, so `make check` passes
+  on a stock `go install` host; `script/bootstrap` and the `Dockerfile`
+  test image no longer install it, and a new test asserts the uploaded
+  database keeps no pages from deleted rows. Dropped the now-false note
+  on the 2026-08-07 entry below that said bootstrap installs it.
 - 2026-09-21: Made `.gitea/workflows/check.yml` run on pushes to `main`
   and `next` and on pull requests against either, so unit PRs (whose
   base is `next`) and `next` itself get a CI run instead of relying on a
@@ -529,7 +537,7 @@ release" is exactly the contradiction
   was green was wrong.
 - 2026-08-07: Added the standard `.golangci.yml` and `.editorconfig`
   (issue #59); lint findings under the new config are tracked in issue
-  #61. `script/bootstrap` now installs sqlite3 (needed by tests).
+  #61.
 - 2026-07-07 Adopted scripts-to-rule-them-all: `script/` entrypoints,
   Makefile shims, README Entrypoints section
 - 2026-07-02: Consolidated CLI verbs, retired overlapping commands; bound

docs/DATAMODEL.md

@@ -192,7 +192,7 @@ Tracks blob upload metrics.
 After a snapshot is completed:
 1. Copy database to temporary file
 2. Clean temporary database to contain only current snapshot data
-3. Export to SQL dump using sqlite3
+3. VACUUM the trimmed database so deleted rows leave no pages behind
 4. Compress with zstd and encrypt with age
 5. Upload to S3 as `metadata/{snapshot-id}/db.zst.age`
 6. Generate blob manifest and upload as `metadata/{snapshot-id}/manifest.json.zst`

internal/snapshot/snapshot.go

@@ -44,7 +44,6 @@ import (
 	"errors"
 	"fmt"
 	"io"
-	"os/exec"
 	"path/filepath"
 	"strings"
 	"time"
@@ -669,14 +668,31 @@ func (sm *SnapshotManager) collectCleanupStats(
 
 // vacuumDatabase runs VACUUM on the database to remove deleted data and compact
 // This is critical for security - ensures no stale/deleted data pages are uploaded
+//
+// VACUUM runs through the modernc.org/sqlite driver, on a freshly opened
+// connection with no transaction in flight (VACUUM cannot run inside one).
+// The database opens in WAL mode, so VACUUM's rewrite lands in the WAL; the
+// checkpoint on Close flushes it into the main file, which is the file we
+// then compress and upload.
 func (sm *SnapshotManager) vacuumDatabase(ctx context.Context, dbPath string) error {
 	log.Debug("Running VACUUM on database", "path", dbPath)
-	//nolint:gosec // G204: fixed argv; dbPath is our own temp file path
-	cmd := exec.CommandContext(ctx, "sqlite3", dbPath, "VACUUM;")
 
-	output, err := cmd.CombinedOutput()
+	db, err := database.New(ctx, dbPath)
 	if err != nil {
-		return fmt.Errorf("running VACUUM: %w (output: %s)", err, string(output))
+		return fmt.Errorf("opening database for VACUUM: %w", err)
+	}
+
+	defer func() {
+		cerr := db.Close()
+		if cerr != nil {
+			log.Debug("Failed to close database after VACUUM",
+				"path", dbPath, "error", cerr)
+		}
+	}()
+
+	_, err = db.ExecWithLog(ctx, "VACUUM")
+	if err != nil {
+		return fmt.Errorf("running VACUUM: %w", err)
 	}
 
 	return nil

internal/snapshot/snapshot_test.go

@@ -2,6 +2,7 @@
 package snapshot
 
 import (
+	"bytes"
 	"context"
 	"database/sql"
 	"io"
@@ -96,6 +97,97 @@ func verifyCleanedDB(
 	}
 }
 
+// TestVacuumDatabaseRemovesDeletedData proves the export path uploads a
+// compacted database: after rows carrying a recognizable marker are deleted
+// and vacuumDatabase runs, no page holding that marker survives in the file
+// on disk (the file compressFile later reads for upload).
+func TestVacuumDatabaseRemovesDeletedData(t *testing.T) {
+	log.Initialize(log.Config{})
+	t.Parallel()
+
+	ctx := context.Background()
+	fs := afero.NewOsFs()
+
+	tempDir := t.TempDir()
+	dbPath := filepath.Join(tempDir, "snapshot.db")
+
+	db, err := database.New(ctx, dbPath)
+	if err != nil {
+		t.Fatalf("failed to create database: %v", err)
+	}
+
+	// A marker distinctive enough that its presence in the raw file can only
+	// come from the rows inserted below.
+	marker := []byte("VACUUM_PROBE_DEADBEEF_DELETED_ROW")
+	payload := bytes.Repeat(marker, 128) // ~4 KiB per row
+
+	_, err = db.Conn().ExecContext(ctx,
+		"CREATE TABLE vacuum_probe (id INTEGER PRIMARY KEY, payload BLOB)")
+	if err != nil {
+		t.Fatalf("failed to create probe table: %v", err)
+	}
+
+	for range 512 {
+		_, err = db.Conn().ExecContext(ctx,
+			"INSERT INTO vacuum_probe (payload) VALUES (?)", payload)
+		if err != nil {
+			t.Fatalf("failed to insert probe row: %v", err)
+		}
+	}
+
+	_, err = db.Conn().ExecContext(ctx, "DELETE FROM vacuum_probe")
+	if err != nil {
+		t.Fatalf("failed to delete probe rows: %v", err)
+	}
+
+	// Close so the deletes reach the main file, mirroring the state
+	// prepareExportDB hands to vacuumDatabase.
+	err = db.Close()
+	if err != nil {
+		t.Fatalf("failed to close database: %v", err)
+	}
+
+	beforeInfo, err := fs.Stat(dbPath)
+	if err != nil {
+		t.Fatalf("failed to stat database before vacuum: %v", err)
+	}
+
+	beforeBytes, err := afero.ReadFile(fs, dbPath)
+	if err != nil {
+		t.Fatalf("failed to read database before vacuum: %v", err)
+	}
+
+	if !bytes.Contains(beforeBytes, marker) {
+		t.Fatalf("expected deleted-row data to linger before vacuum")
+	}
+
+	sm := &SnapshotManager{fs: fs}
+
+	err = sm.vacuumDatabase(ctx, dbPath)
+	if err != nil {
+		t.Fatalf("vacuumDatabase failed: %v", err)
+	}
+
+	afterBytes, err := afero.ReadFile(fs, dbPath)
+	if err != nil {
+		t.Fatalf("failed to read database after vacuum: %v", err)
+	}
+
+	if bytes.Contains(afterBytes, marker) {
+		t.Fatalf("deleted-row data survived vacuum in the uploaded file")
+	}
+
+	afterInfo, err := fs.Stat(dbPath)
+	if err != nil {
+		t.Fatalf("failed to stat database after vacuum: %v", err)
+	}
+
+	if afterInfo.Size() >= beforeInfo.Size() {
+		t.Fatalf("expected vacuum to shrink the file: before=%d after=%d",
+			beforeInfo.Size(), afterInfo.Size())
+	}
+}
+
 func TestCleanSnapshotDBEmptySnapshot(t *testing.T) {
 	// Initialize logger
 	log.Initialize(log.Config{})

script/bootstrap

@@ -114,9 +114,6 @@ main() {
     # from CI. Nothing on the host is ever used as a linter, at any
     # version, so installing one here would buy nothing.
 
-    # sqlite3 CLI: the test suite shells out to it (VACUUM).
-    if missing sqlite3; then pkg_install sqlite sqlite3 sqlite sqlite; fi
-
     # goreleaser, at the version pinned by script/install-goreleaser and
     # verified against a hardcoded sha256. Package managers are not used
     # for it: they ship whatever version they happen to carry, and the