Update project documentation to application.yaml

It appears the project recently started using application.yaml instead of .properties. Updated the main doc files to avoid confusion with future newcomers. Also, stale_outputs_checked is a marker file produced by intellij and should be gitignored.

.gitignore

@@ -5,6 +5,7 @@ build/
 bin/
 out/
 lib/
+stale_outputs_checked
 
 # Maven
 target/