Bash oneliner command which uses detox to clear svn repository with calling svn mv command (updating references instead of removing and adding same file once again). Replace svn with git or anything else if needed.
yourRepo>$ detox -nr * | sed -E 's/(.*) -> (.*)/svn mv \"\1\" \"\2\"/' | sh
As this is dumb oneliner it might require to be ran couple times (if parent references already were changed due ran).