If I try to update my subversion repo, it says I must run cleanup. If I run cleanup, it says a file is missing. (I deleted a MASSIVE directory of files that failed to commit
I got the same problem, in my case I was using svn tortoise with the application I mean. Using the cmd shell of windows in root mode I applied svn cleanup and then svn update.... Then you can comeback to the application mode aand it will work perfectly!