SVN stores the entire history of not just each individual file, but also of how they were arranged into a hierarchical directory structure. When you decide to move a file (or subdirectory) to a new place in the tree structure, SVN can move that file's history along with it. (That means that when somebody wonders what this "new" file is doing there, they'll be able to trace its origin back to the old days before you made this move, or a complete history of its names, locations, and commit logs for changes.)
In order for all this to work, SVN has to know that the move is happening, which means that you have to do the move through an SVN client:
svn mv
SC Plugin currently doesn't support move or delete at all
SVNx is decent
The command line works well if you can handle Unix directory notation.
