Abakt is a thoroughly competent, free backup manager, but it can also be used to manipulate file and directory structures through it's very flexible filtering mechanisms.

For example, one useful trick I've found is to add this filter over a development directory if I want a copy of my code without all the '.svn' directories. Excluding a directory matching a mask isn't specifically mentioned in the documentation, so I'll reproduce the pattern here:

  FilterSet:

  Action:    Exclude
  Path Mask: *\.svn\*|*