Files not longer under version control, after refresh in Eclipse

"yes, you need to upgrade your subclipse plugin & svn connectors, either javahl (1.6.x) or svnkit (1.3.x) so they match support your installed subversion (1.6.5). See the project site for the upgrade site URLs if you don't have these already.

Or downgrade your ubuntu subversion package, but I would not recommend doing that."