Remove Version class from console application and docs

This should have been done with 18590f49bff8272bc77bb1849ffd2b54c952c3d5
Revise console application and documentation

Replace trivial odm:query example with an explanation of where to find the reference implementation and how to proceed with configuration.
Merge pull request #894 from doctrine/doc-console-commands

Remove Version class refs and revise console command docs