I find in docs that it is possible to override conf files in webapps/alfresco… tree using the ones in shared/classes/alfresco/extension. But when I (create and/or) change, for example repository.properties or log4j.properties files I still got errors until I change the other ones.
You can override default properties by changing content of custom-repository.properties file in extension directory. To include any other property file in bootstrap process you will have to change custom-repository-context.xml spring configuration file which is also placed in extensions directory