if you have the patience or not have too many of them folders you can right click it in the navigator view and make sure to check the derived property.
This should cause eclipse to ignore these folders.
...hmmm... wait a minute... you said you shuffled a lot of stuff around.... did you do this through windows explorer or inside eclipse ?
There are commands in SVN to move folders that are under source control, if you do not use them you run the chance that SVN will not recognized these folders from their original and will loos history attached to the file itself. worst somethins I got some weird side effects where the only solution was to
- delete all the .svn folders
- copy all the source elsewhere
- do a checkout from scratch
- overwrite the files from repository with backup in 2
- checkin
Then I did the rearrangement from eclipse or directly in the SVN through the SVN repository explorer and started working again with a new checkout.
Usually eclipse deals fairly well with these .svn folders but in some rare occasion it gets all out of whack and I had to start from scratch, sometimes reinstalling eclipse from pulse directly (try pulse it's definitively worth it, reinstalling your environment from scratch on a new system is but a few clicks).
Anyhow.. hope this helps... good luck