Fix daemon race condition: prevent stale exports

- Add JSONL timestamp check in validatePreExport
- Refuse export if JSONL is newer than database
- Force daemon to import before exporting when JSONL updated
- Add test case for JSONL-newer-than-DB scenario
- Fixes bd-89e2

cmd/bd/integrity.go

@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"math"
 	"os"
+	"path/filepath"
 
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/types"
@@ -14,6 +15,20 @@ import (
 // validatePreExport performs integrity checks before exporting database to JSONL.
 // Returns error if critical issues found that would cause data loss.
 func validatePreExport(ctx context.Context, store storage.Storage, jsonlPath string) error {
+	// Check if JSONL is newer than database - if so, must import first
+	jsonlInfo, jsonlStatErr := os.Stat(jsonlPath)
+	if jsonlStatErr == nil {
+		beadsDir := filepath.Dir(jsonlPath)
+		dbPath := filepath.Join(beadsDir, "beads.db")
+		dbInfo, dbStatErr := os.Stat(dbPath)
+		if dbStatErr == nil {
+			// If JSONL is newer, refuse export - caller must import first
+			if jsonlInfo.ModTime().After(dbInfo.ModTime()) {
+				return fmt.Errorf("refusing to export: JSONL is newer than database (import first to avoid data loss)")
+			}
+		}
+	}
+
 	// Get database issue count (fast path with COUNT(*) if available)
 	dbCount, err := countDBIssuesFast(ctx, store)
 	if err != nil {
@@ -22,13 +37,12 @@ func validatePreExport(ctx context.Context, store storage.Storage, jsonlPath str
 
 	// Get JSONL issue count
 	jsonlCount := 0
-	fileInfo, statErr := os.Stat(jsonlPath)
+	if jsonlStatErr == nil {
-	if statErr == nil {
 		jsonlCount, err = countIssuesInJSONL(jsonlPath)
 		if err != nil {
 			// Conservative: if JSONL exists with content but we can't count it,
 			// and DB is empty, refuse to export (potential data loss)
-			if dbCount == 0 && fileInfo.Size() > 0 {
+			if dbCount == 0 && jsonlInfo.Size() > 0 {
 				return fmt.Errorf("refusing to export empty DB over existing JSONL whose contents couldn't be verified: %w", err)
 			}
 			// Warning for other cases

cmd/bd/integrity_test.go

@@ -4,7 +4,9 @@ import (
 	"context"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
+	"time"
 
 	"github.com/steveyegge/beads/internal/types"
 )
@@ -111,6 +113,55 @@ func TestValidatePreExport(t *testing.T) {
 			t.Error("Expected error for empty DB over unreadable non-empty JSONL, got nil")
 		}
 	})
+
+	t.Run("JSONL newer than DB fails", func(t *testing.T) {
+		// Create temp directory
+		tmpDir := t.TempDir()
+		beadsDir := filepath.Join(tmpDir, ".beads")
+		if err := os.MkdirAll(beadsDir, 0755); err != nil {
+			t.Fatalf("Failed to create .beads dir: %v", err)
+		}
+		dbPath := filepath.Join(beadsDir, "beads.db")
+		jsonlPath := filepath.Join(beadsDir, "beads.jsonl")
+
+		// Create database with issue
+		store := newTestStoreWithPrefix(t, dbPath, "bd")
+		ctx := context.Background()
+		issue := &types.Issue{
+			ID:          "bd-1",
+			Title:       "Test",
+			Status:      types.StatusOpen,
+			Priority:    1,
+			IssueType:   types.TypeTask,
+			Description: "Test issue",
+		}
+		if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+			t.Fatalf("Failed to create issue: %v", err)
+		}
+
+		// Create JSONL file with newer timestamp
+		jsonlContent := `{"id":"bd-1","title":"Test","status":"open","priority":1}
+`
+		if err := os.WriteFile(jsonlPath, []byte(jsonlContent), 0600); err != nil {
+			t.Fatalf("Failed to write JSONL: %v", err)
+		}
+
+		// Touch JSONL to make it newer than DB
+		// (in real scenario, this happens when git pull updates JSONL but daemon hasn't imported yet)
+		futureTime := time.Now().Add(1 * time.Second)
+		if err := os.Chtimes(jsonlPath, futureTime, futureTime); err != nil {
+			t.Fatalf("Failed to touch JSONL: %v", err)
+		}
+
+		// Should fail validation (JSONL is newer, must import first)
+		err := validatePreExport(ctx, store, jsonlPath)
+		if err == nil {
+			t.Error("Expected error for JSONL newer than DB, got nil")
+		}
+		if err != nil && !strings.Contains(err.Error(), "JSONL is newer than database") {
+			t.Errorf("Expected 'JSONL is newer' error, got: %v", err)
+		}
+	})
 }
 
 func TestValidatePostImport(t *testing.T) {