We are currently shipping a confluence jar in the WEB-INF/lib of the standalone distribution. This shouldn't have any effect other than increasing the size of the distribution. This is because classes in WEB-INF/classes should override those in the jar as per the servlet spec. We should stop this from happening regardless.

An interesting point was raised about shipping the jar without classes in WEB-INF/classes. Patches could be unpacked to classes which would let us see at a glance what mods had been made to a Confluence instance.