Better error display for eXide (Adam -> Closes #358)

removed IO so that if something breaks eXide now display where it broke
[refactor] Moved package org.exist.dom -> org.exist.dom.persistent
[refactor] Moved package org.exist.memtree -> org.exist.dom.memtree
[bugfix] First pass at extracting interfaces for Stored Nodes
Remove dead code
This was previously marked as @deprecated by Dmitriy, however no
alternative was ever forthcoming and so it is not deprecated (I have
discussed this with Dmitriy)