fix(api): exclude soft-deleted records from pagination Count queries

The Count methods in note, document, asset, and repository GORM stores
did not filter out soft-deleted records (deleted_at IS NULL), while their
corresponding List methods did. This mismatch caused the total count in
pagination responses to be higher than the actual returnable items,
which could cause clients to paginate infinitely when offset >= total.

Fixes #222

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: ericfitz

.version

@@ -1,6 +1,6 @@
 {
   "major": 1,
   "minor": 3,
-  "patch": 2,
+  "patch": 3,
   "prerelease": ""
 }

api/asset_store_gorm.go

@@ -569,9 +569,13 @@ func (s *GormAssetStore) Count(ctx context.Context, threatModelID string) (int,
 	logger.Debug("Counting assets for threat model %s", threatModelID)
 
 	var count int64
-	result := s.db.WithContext(ctx).Model(&models.Asset{}).
-		Where("threat_model_id = ?", threatModelID).
-		Count(&count)
+	query := s.db.WithContext(ctx).Model(&models.Asset{})
+	if includeDeletedFromContext(ctx) {
+		query = query.Where("threat_model_id = ?", threatModelID)
+	} else {
+		query = query.Where("threat_model_id = ? AND deleted_at IS NULL", threatModelID)
+	}
+	result := query.Count(&count)
 
 	if result.Error != nil {
 		logger.Error("Failed to count assets: %v", result.Error)

api/document_store_gorm.go

@@ -456,9 +456,13 @@ func (s *GormDocumentStore) Count(ctx context.Context, threatModelID string) (in
 	logger.Debug("Counting documents for threat model %s", threatModelID)
 
 	var count int64
-	result := s.db.WithContext(ctx).Model(&models.Document{}).
-		Where("threat_model_id = ?", threatModelID).
-		Count(&count)
+	query := s.db.WithContext(ctx).Model(&models.Document{})
+	if includeDeletedFromContext(ctx) {
+		query = query.Where("threat_model_id = ?", threatModelID)
+	} else {
+		query = query.Where("threat_model_id = ? AND deleted_at IS NULL", threatModelID)
+	}
+	result := query.Count(&count)
 
 	if result.Error != nil {
 		logger.Error("Failed to count documents: %v", result.Error)

api/note_store_gorm.go

@@ -397,9 +397,13 @@ func (s *GormNoteStore) Count(ctx context.Context, threatModelID string) (int, e
 	logger.Debug("Counting notes for threat model %s", threatModelID)
 
 	var count int64
-	result := s.db.WithContext(ctx).Model(&models.Note{}).
-		Where("threat_model_id = ?", threatModelID).
-		Count(&count)
+	query := s.db.WithContext(ctx).Model(&models.Note{})
+	if includeDeletedFromContext(ctx) {
+		query = query.Where("threat_model_id = ?", threatModelID)
+	} else {
+		query = query.Where("threat_model_id = ? AND deleted_at IS NULL", threatModelID)
+	}
+	result := query.Count(&count)
 
 	if result.Error != nil {
 		logger.Error("Failed to count notes: %v", result.Error)

api/repository_store_gorm.go

@@ -510,9 +510,13 @@ func (s *GormRepositoryStore) Count(ctx context.Context, threatModelID string) (
 	logger.Debug("Counting repositories for threat model %s", threatModelID)
 
 	var count int64
-	result := s.db.WithContext(ctx).Model(&models.Repository{}).
-		Where("threat_model_id = ?", threatModelID).
-		Count(&count)
+	query := s.db.WithContext(ctx).Model(&models.Repository{})
+	if includeDeletedFromContext(ctx) {
+		query = query.Where("threat_model_id = ?", threatModelID)
+	} else {
+		query = query.Where("threat_model_id = ? AND deleted_at IS NULL", threatModelID)
+	}
+	result := query.Count(&count)
 
 	if result.Error != nil {
 		logger.Error("Failed to count repositories: %v", result.Error)

api/version.go

@@ -50,7 +50,7 @@ var (
 	// Minor version number
 	VersionMinor = "3"
 	// Patch version number
-	VersionPatch = "2"
+	VersionPatch = "3"
 	// VersionPreRelease is the pre-release label (e.g., "rc.0", "beta.1"), empty for stable releases
 	VersionPreRelease = ""
 	// GitCommit is the git commit hash from build