SVN was not intended for this, ideally you should check in an empty directory. Looking back, 20/20, so now you need to hack.
Create an empty branch in your repo, svn switch to this branch. This will update your working copy in this branch, in which there is nothing, so any files under version control should be deleted from your working copy. This will leave files and folders of .svn metafiles that you can work with individually, which will be much easier than individually figuring out which files are under version control and which are not
Also, if your SVN story has revision 1 as a new empty repo, you can SVN Update to this revision, which will do the same as the switching maneuver above, but most of the repos I've dealt with already have a lot files in version 1.
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