R – how to integrate a branch into a trunk if the folder structure has changed

I couldn't properly follow the other answers, here's more of a dummies guide...

You can do this either way round to go trunk -> branch or branch -> trunk. I always first do trunk -> branch fix any conflicts there and then merge branch -> trunk.

Merge trunk into a branch / tag

1. Checkout the branch / tag
2. Right-click on the root of the branch | Tortoise SVN | Merge ...
3. Merge Type: Merge a range of revisions | Click 'Next'
4. Merge revision range: Select the URL of the trunk directory that you copied to the branch / tag. Enter the revisions to merge or leave the field empty to merge all revisions | click 'Next'
5. Merge options: I just left these as default | click 'Merge'
6. This will merge the revisions into the checked out branch / tag
7. Then commit the merged changes to the branch / tag

Use svn move to move the contents of the old trunk somewhere else and rename the branch to trunk afterward.

Note that copy and move in svn work like file operations. You can use them to move/copy stuff around in your repository and these changes are versioned as well. Think of "move" as "copy+delete".

[EDIT] Nilbus just notified me that you will get merge conflicts when you use svn move.

I still think that this is the correct approach. It will cause conflicts but if you merge carefully, chances are that you won't lose any data. If that bothers you, use a better VCS like Mercurial or Git.