Just as get a few steps ahead, I hit something else. Currently if I shutdown my confluence instance, and start up using the supplied catalina.sh (run|stop) I get the following error;
SEVERE: The web application  created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@1e648bd]) and a value of type [org.dom4j.DocumentFactory] (value [org.dom4j.DocumentFactory@1b1acc3]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.log4j:ERROR LogMananger.repositorySelector was null likely due to error in class reloading, using NOPLoggerRepository.
Of course kb says you can ignore it, of course that’s no problem except that when I do get this error after first restart the web application no longer works and I get http 404 type errors. Thus the installation is broken. This error happened right after I got the following one;
org.springframework.dao.DataIntegrityViolationException: Hibernate operation: could not insert: [com.atlassian.confluence.core.BodyContent#98322]; SQL ; Duplicate entry '98322' for key 'PRIMARY'; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry '98322' for key 'PRIMARY' at org.springframework.jdbc.support.SQLStateSQLExceptionTranslator.translate(SQLStateSQLExceptionTranslator.java:110) caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry '98322' for key 'PRIMARY' at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
Which is not fixed by the work around of setting a value in my.cnf as per the kb.
Hopefully we can get the issues resolved, would really like to use confluence with the mysql backend.