Update .gitignore to keep vignettes and paper directories

Author: HzaCode

.gitignore

@@ -23,11 +23,9 @@ tests/test_direct_api_streams.R
 coverage_report.html
 runnable_function_examples.html
 
-# Documentation files (not for GitHub)
-vignettes/
+# User data files (not for GitHub)
 export_data/
 tests/manual_tests/
-paper/
 
 /..Rcheck
 
@@ -40,7 +38,5 @@ test-*.md
 
 # Node modules (if accidentally created)
 node_modules/
-package.json
-package-lock.json
 /doc/
 /Meta/