To see new files/folders just check the box "show unversioned files" at the bottom left of the commit dialog. Then you'll never miss new files. You will still have to add them to be versioned manually, but that can be done from the commit dialog as well (select the files, right-click and choose "add"). As for folders appearing as "deleted": when you delete them without the proper svn command, then of course they will show up like that. Just select them and do a commit so they're also removed from version control.
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