fix: delete document cleans up store files and embeddings

db.go

@@ -381,6 +381,7 @@ func UpdateDocumentMetadata(id string, metadata map[string]string) error {
 // DeleteDocument removes a document from the database
 func DeleteDocument(id string) error {
 	deleteFTS(id)
+	db.Exec(`DELETE FROM embeddings WHERE doc_id = ?`, id)
 	_, err := db.Exec(`DELETE FROM documents WHERE id = ?`, id)
 	return err
 }

main.go

@@ -501,7 +501,7 @@ func deleteDocumentHandler(w http.ResponseWriter, r *http.Request) {
 		return
 	}
 
-	// Delete from database
+	// Delete from database (includes FTS and embeddings)
 	DeleteDocument(id)
 
 	// Delete record file
@@ -509,6 +509,12 @@ func deleteDocumentHandler(w http.ResponseWriter, r *http.Request) {
 		os.Remove(doc.RecordPath)
 	}
 
+	// Delete store files (PDF/TXT)
+	for _, ext := range []string{".pdf", ".txt", ""} {
+		path := filepath.Join(storeDir, id+ext)
+		os.Remove(path) // ignore errors for non-existent files
+	}
+
 	w.Header().Set("Content-Type", "application/json")
 	json.NewEncoder(w).Encode(map[string]string{"status": "deleted"})
 }