It is very cool to have a development environment for Python that is scriptable in Python too. I did some tools in Python to help me working with the Python code itself.
But what I don't like is that the environment is a bit different than the regular Python or Jython environment.These differences are sometimes introducing problems that are hard to solve. I would appreciate a documentation of these differences.
Just saw this thread now and wanted to share that PyDev does already use an internal jython for scripting purposes (so, it calls python code from java inside Eclipse).
Examples of the scripting are in: http://pydev.org/manual_articles_scripting.html
And the actual code that'll call it is available at: https://github.com/aptana/Pydev/blob/master/plugins/org.python.pydev.jython/src/org/python/pydev/jython/JythonPlugin.java -- note that it does some tricks to reload the file if it was changed (and it's tested with Jython 2.1).