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.

src/main/resources/log4j.properties.template

@@ -17,7 +17,7 @@
 #
 
 # Default application properties. These can be overridden at run time from an
-# application.properties file in the same directory as the executable jar.
+# application.yaml file in the same directory as the executable jar.
 
 log4j.rootCategory=INFO, CONSOLE