feat(repo): add soft-delete with status filter to file queries

File repository now filters by status=active in all query methods (FindByID, FindByUserID, FindByParentID, FindByNameAndParent).

Delete now performs soft-delete by setting status to 'user_deleted' instead of physical row deletion.

Add ListIncludeDeleted to UserRepository for admin views of all users.

Add tests: StatusFilter, SoftDelete, DeleteIdempotent, StatusFilterCount.

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

internal/repository/file.go

@@ -43,7 +43,7 @@ func (r *fileRepository) Create(ctx context.Context, file *model.File) error {
 
 func (r *fileRepository) FindByID(ctx context.Context, id string) (*model.File, error) {
 	var file model.File
-	result := r.db.WithContext(ctx).First(&file, "id = ?", id)
+	result := r.db.WithContext(ctx).First(&file, "id = ? AND status = ?", id, model.StatusActive)
 	if errors.Is(result.Error, gorm.ErrRecordNotFound) {
 		return nil, model.ErrNotFound
 	}
@@ -57,11 +57,11 @@ func (r *fileRepository) FindByUserID(ctx context.Context, userID string, offset
 	var files []model.File
 	var total int64
 
-	if err := r.db.WithContext(ctx).Model(&model.File{}).Where("user_id = ?", userID).Count(&total).Error; err != nil {
+	if err := r.db.WithContext(ctx).Model(&model.File{}).Where("user_id = ? AND status = ?", userID, model.StatusActive).Count(&total).Error; err != nil {
 		return nil, 0, err
 	}
 
-	result := r.db.WithContext(ctx).Where("user_id = ?", userID).Offset(offset).Limit(limit).Find(&files)
+	result := r.db.WithContext(ctx).Where("user_id = ? AND status = ?", userID, model.StatusActive).Offset(offset).Limit(limit).Find(&files)
 	if result.Error != nil {
 		return nil, 0, result.Error
 	}
@@ -71,7 +71,7 @@ func (r *fileRepository) FindByUserID(ctx context.Context, userID string, offset
 
 func (r *fileRepository) FindByParentID(ctx context.Context, userID string, parentID *string) ([]model.File, error) {
 	var files []model.File
-	result := r.db.WithContext(ctx).Where("user_id = ? AND parent_id IS ?", userID, parentID).Find(&files)
+	result := r.db.WithContext(ctx).Where("user_id = ? AND parent_id IS ? AND status = ?", userID, parentID, model.StatusActive).Find(&files)
 	if result.Error != nil {
 		return nil, result.Error
 	}
@@ -82,11 +82,11 @@ func (r *fileRepository) FindByParentIDPaginated(ctx context.Context, userID str
 	var files []model.File
 	var total int64
 
-	if err := r.db.WithContext(ctx).Model(&model.File{}).Where("user_id = ? AND parent_id IS ?", userID, parentID).Count(&total).Error; err != nil {
+	if err := r.db.WithContext(ctx).Model(&model.File{}).Where("user_id = ? AND parent_id IS ? AND status = ?", userID, parentID, model.StatusActive).Count(&total).Error; err != nil {
 		return nil, 0, err
 	}
 
-	result := r.db.WithContext(ctx).Where("user_id = ? AND parent_id IS ?", userID, parentID).Offset(offset).Limit(limit).Order("is_dir DESC, name ASC").Find(&files)
+	result := r.db.WithContext(ctx).Where("user_id = ? AND parent_id IS ? AND status = ?", userID, parentID, model.StatusActive).Offset(offset).Limit(limit).Order("is_dir DESC, name ASC").Find(&files)
 	if result.Error != nil {
 		return nil, 0, result.Error
 	}
@@ -96,7 +96,7 @@ func (r *fileRepository) FindByParentIDPaginated(ctx context.Context, userID str
 
 func (r *fileRepository) FindByNameAndParent(ctx context.Context, userID string, parentID *string, name string) (*model.File, error) {
 	var file model.File
-	result := r.db.WithContext(ctx).Where("user_id = ? AND parent_id IS ? AND name = ?", userID, parentID, name).First(&file)
+	result := r.db.WithContext(ctx).Where("user_id = ? AND parent_id IS ? AND name = ? AND status = ?", userID, parentID, name, model.StatusActive).First(&file)
 	if errors.Is(result.Error, gorm.ErrRecordNotFound) {
 		return nil, model.ErrNotFound
 	}
@@ -115,7 +115,7 @@ func (r *fileRepository) Update(ctx context.Context, file *model.File) error {
 }
 
 func (r *fileRepository) Delete(ctx context.Context, id string) error {
-	result := r.db.WithContext(ctx).Delete(&model.File{}, "id = ?", id)
+	result := r.db.WithContext(ctx).Model(&model.File{}).Where("id = ?", id).Update("status", model.StatusUserDeleted)
 	if result.Error != nil {
 		return result.Error
 	}

internal/repository/file_test.go

@@ -33,6 +33,7 @@ func TestFileRepository_Create(t *testing.T) {
 		UserID: "user-1",
 		Name:   "test.txt",
 		Size:   1024,
+		Status: model.StatusActive,
 	}
 
 	if err := repo.Create(ctx, file); err != nil {
@@ -48,6 +49,7 @@ func TestFileRepository_FindByID(t *testing.T) {
 		ID:     "file-1",
 		UserID: "user-1",
 		Name:   "test.txt",
+		Status: model.StatusActive,
 	}
 	if err := repo.Create(ctx, file); err != nil {
 		t.Fatalf("Create = %v", err)
@@ -77,9 +79,9 @@ func TestFileRepository_FindByUserID(t *testing.T) {
 	ctx := context.Background()
 
 	files := []*model.File{
-		{ID: "f-1", UserID: "user-1", Name: "a.txt"},
+		{ID: "f-1", UserID: "user-1", Name: "a.txt", Status: model.StatusActive},
-		{ID: "f-2", UserID: "user-1", Name: "b.txt"},
+		{ID: "f-2", UserID: "user-1", Name: "b.txt", Status: model.StatusActive},
-		{ID: "f-3", UserID: "user-2", Name: "c.txt"},
+		{ID: "f-3", UserID: "user-2", Name: "c.txt", Status: model.StatusActive},
 	}
 	for _, f := range files {
 		if err := repo.Create(ctx, f); err != nil {
@@ -105,9 +107,9 @@ func TestFileRepository_FindByParentID(t *testing.T) {
 
 	parentID := "dir-1"
 	files := []*model.File{
-		{ID: "f-1", UserID: "user-1", ParentID: &parentID, Name: "a.txt"},
+		{ID: "f-1", UserID: "user-1", ParentID: &parentID, Name: "a.txt", Status: model.StatusActive},
-		{ID: "f-2", UserID: "user-1", ParentID: &parentID, Name: "b.txt"},
+		{ID: "f-2", UserID: "user-1", ParentID: &parentID, Name: "b.txt", Status: model.StatusActive},
-		{ID: "f-3", UserID: "user-1", Name: "c.txt"},
+		{ID: "f-3", UserID: "user-1", Name: "c.txt", Status: model.StatusActive},
 	}
 	for _, f := range files {
 		if err := repo.Create(ctx, f); err != nil {
@@ -130,8 +132,8 @@ func TestFileRepository_FindByParentIDNull(t *testing.T) {
 
 	parentID := "dir-1"
 	files := []*model.File{
-		{ID: "f-1", UserID: "user-1", ParentID: &parentID, Name: "a.txt"},
+		{ID: "f-1", UserID: "user-1", ParentID: &parentID, Name: "a.txt", Status: model.StatusActive},
-		{ID: "f-2", UserID: "user-1", Name: "root.txt"},
+		{ID: "f-2", UserID: "user-1", Name: "root.txt", Status: model.StatusActive},
 	}
 	for _, f := range files {
 		if err := repo.Create(ctx, f); err != nil {
@@ -152,7 +154,7 @@ func TestFileRepository_Update(t *testing.T) {
 	repo := setupFileRepo(t)
 	ctx := context.Background()
 
-	file := &model.File{ID: "file-1", UserID: "user-1", Name: "original.txt"}
+	file := &model.File{ID: "file-1", UserID: "user-1", Name: "original.txt", Status: model.StatusActive}
 	if err := repo.Create(ctx, file); err != nil {
 		t.Fatalf("Create = %v", err)
 	}
@@ -179,7 +181,7 @@ func TestFileRepository_Delete(t *testing.T) {
 	repo := setupFileRepo(t)
 	ctx := context.Background()
 
-	file := &model.File{ID: "file-1", UserID: "user-1", Name: "test.txt"}
+	file := &model.File{ID: "file-1", UserID: "user-1", Name: "test.txt", Status: model.StatusActive}
 	if err := repo.Create(ctx, file); err != nil {
 		t.Fatalf("Create = %v", err)
 	}
@@ -193,3 +195,121 @@ func TestFileRepository_Delete(t *testing.T) {
 		t.Fatalf("expected ErrNotFound after delete, got %v", err)
 	}
 }
+
+func TestFileRepository_SoftDelete(t *testing.T) {
+	repo := setupFileRepo(t)
+	ctx := context.Background()
+
+	file := &model.File{
+		ID:     "file-1",
+		UserID: "user-1",
+		Name:   "test.txt",
+		Status: model.StatusActive,
+	}
+	if err := repo.Create(ctx, file); err != nil {
+		t.Fatalf("Create = %v", err)
+	}
+
+	if err := repo.Delete(ctx, "file-1"); err != nil {
+		t.Fatalf("Delete = %v", err)
+	}
+
+	_, err := repo.FindByID(ctx, "file-1")
+	if err != model.ErrNotFound {
+		t.Fatalf("expected ErrNotFound after soft-delete, got %v", err)
+	}
+}
+
+func TestFileRepository_StatusFilter(t *testing.T) {
+	repo := setupFileRepo(t)
+	ctx := context.Background()
+
+	activeFile := &model.File{
+		ID:     "f-1",
+		UserID: "user-1",
+		Name:   "active.txt",
+		Status: model.StatusActive,
+	}
+	deletedFile := &model.File{
+		ID:     "f-2",
+		UserID: "user-1",
+		Name:   "deleted.txt",
+		Status: model.StatusUserDeleted,
+	}
+
+	if err := repo.Create(ctx, activeFile); err != nil {
+		t.Fatalf("Create active = %v", err)
+	}
+	if err := repo.Create(ctx, deletedFile); err != nil {
+		t.Fatalf("Create deleted = %v", err)
+	}
+
+	result, total, err := repo.FindByUserID(ctx, "user-1", 0, 10)
+	if err != nil {
+		t.Fatalf("FindByUserID = %v", err)
+	}
+	if len(result) != 1 {
+		t.Errorf("len(result) = %d, want 1", len(result))
+	}
+	if total != 1 {
+		t.Errorf("total = %d, want 1", total)
+	}
+	if result[0].ID != "f-1" {
+		t.Errorf("result[0].ID = %q, want %q", result[0].ID, "f-1")
+	}
+}
+
+func TestFileRepository_DeleteIdempotent(t *testing.T) {
+	repo := setupFileRepo(t)
+	ctx := context.Background()
+
+	file := &model.File{
+		ID:     "file-1",
+		UserID: "user-1",
+		Name:   "test.txt",
+		Status: model.StatusActive,
+	}
+	if err := repo.Create(ctx, file); err != nil {
+		t.Fatalf("Create = %v", err)
+	}
+
+	if err := repo.Delete(ctx, "file-1"); err != nil {
+		t.Fatalf("first Delete = %v", err)
+	}
+	if err := repo.Delete(ctx, "file-1"); err != nil {
+		t.Fatalf("second Delete = %v", err)
+	}
+}
+
+func TestFileRepository_StatusFilterCount(t *testing.T) {
+	repo := setupFileRepo(t)
+	ctx := context.Background()
+
+	activeFile := &model.File{
+		ID:     "f-1",
+		UserID: "user-1",
+		Name:   "active.txt",
+		Status: model.StatusActive,
+	}
+	deletedFile := &model.File{
+		ID:     "f-2",
+		UserID: "user-1",
+		Name:   "deleted.txt",
+		Status: model.StatusUserDeleted,
+	}
+
+	if err := repo.Create(ctx, activeFile); err != nil {
+		t.Fatalf("Create active = %v", err)
+	}
+	if err := repo.Create(ctx, deletedFile); err != nil {
+		t.Fatalf("Create deleted = %v", err)
+	}
+
+	_, total, err := repo.FindByUserID(ctx, "user-1", 0, 10)
+	if err != nil {
+		t.Fatalf("FindByUserID = %v", err)
+	}
+	if total != 1 {
+		t.Errorf("total = %d, want 1 (soft-deleted excluded from count)", total)
+	}
+}

internal/repository/user.go

@@ -25,6 +25,7 @@ type UserRepository interface {
 	Update(ctx context.Context, user *model.User) error
 	Delete(ctx context.Context, id string) error
 	List(ctx context.Context, offset, limit int) ([]model.User, int64, error)
+	ListIncludeDeleted(ctx context.Context, offset, limit int) ([]model.User, int64, error)
 }
 
 type userRepository struct {
@@ -130,3 +131,20 @@ func (r *userRepository) List(ctx context.Context, offset, limit int) ([]model.U
 
 	return users, total, nil
 }
+
+// ListIncludeDeleted returns all users (including soft-deleted), paginated.
+func (r *userRepository) ListIncludeDeleted(ctx context.Context, offset, limit int) ([]model.User, int64, error) {
+	var users []model.User
+	var total int64
+
+	if err := r.db.WithContext(ctx).Model(&model.User{}).Count(&total).Error; err != nil {
+		return nil, 0, err
+	}
+
+	result := r.db.WithContext(ctx).Offset(offset).Limit(limit).Find(&users)
+	if result.Error != nil {
+		return nil, 0, result.Error
+	}
+
+	return users, total, nil
+}