feat: Update .gitignore and refine TypeScript configuration; clean up commented code and enhance dataset validation; npm updates

- Updated .gitignore to include new patterns
- Refined TypeScript configuration for better performance and readability
- Cleaned up commented code in several files
- Enhanced dataset validation logic
- Updated npm dependencies to the latest versions

app/validators/dataset.ts

@@ -273,7 +273,7 @@ export const updateDatasetValidator = vine.compile(
         references: vine
             .array(
                 vine.object({
-                    value: vine.string().trim().minLength(3).maxLength(255),
+                    value: vine.string().trim().minLength(3).maxLength(255).validateReference({ typeField: 'type' }),
                     type: vine.enum(Object.values(ReferenceIdentifierTypes)),
                     relation: vine.enum(Object.values(RelationTypes)),
                     label: vine.string().trim().minLength(2).maxLength(255),