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 stop installing
the CLI in both the test-build and the shipped runtime stage, so the
image no longer carries the dependency this change removes.

Model: opus-4-8

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