[#2002] multiple clean ups for 4.0.0

- Create a meta directory for our merge notes and how to release.
- Clean up an extra newline in irods_setup.pl
- Add a known issue around 3.x->4.0+ iCommands
- Add hashing updates to the manual
[#2011] [#2009] upgrade sql and packaging
[#2002] upgrade steps reshuffling
[#2012] remove rcore_ tables and all code mentioning them