<p>I would like to automatically convert between tabs and spaces for indentation when I commit/update code to/from our repository. I have found the AnyEdit plugin for eclipse, which can convert directories of files. Not bad for a start, but does anybody have more expierience on how to handle this? Or maybe know of an Ant script or something else?</p>

Why not just use the code formatter and/or cleanup function? It has settings that take care of that stuff for you. You can even have it run automatically on save.
Edit:
As Peter Perháč points out in the comments, this only answers half the question. I don't have any practical experience, but you could try the
Maven Eclipse Format Plugin
to format from a Maven build.
Unfortunately, that's Maven only, and I know of no light-weight command line formatter. But if you happen to use Maven, you can bind the format goal to the proper phase, and if you set Eclipse to auto-build, it would format on update.
Depending on the SCM tool (git, svn, etc), you could also create a hook that runs the build (but it might be a bit too heavy-weight for that).