Fix directory permission issue in the MB pack

Before this fix some directories including the parent directory was given read
write permission to all the users (i.e. 777). Adding the version to
maven-assembly-plugin fixed the issue. But after the ading version axis2.xml
was added to the MB zip twice. The extra copying was exclude in bin.xml to
avoid this. Also the version number of log4j was removed from the
distribution/pom.xml. Now the version is inherited from parent pom and
therefore log4j version conflicts are avoided.