Update setup.py to reflect re-factored setup code for 0.2 release

This implements the latest changes to the package template based on the latest refactoring by @iguananaut. There is currently an issue to do with the configuration file generation if one tries to install the package template::

```
regenerating default packagename.cfg file
copying ../../../../../Library/Python/3.2/lib/python/site-packages/astropy-0.3.dev2997-py3.2-macosx-10.6-x86_64.egg/astropy/config/packagename.cfg -> build/lib.macosx-10.6-x86_64-3.2/../../../../../Library/Python/3.2/lib/python/site-packages/astropy-0.3.dev2997-py3.2-macosx-10.6-x86_64.egg/astropy/config
error: build/lib.macosx-10.6-x86_64-3.2/../../../../../Library/Python/3.2/lib/python/site-packages/astropy-0.3.dev2997-py3.2-macosx-10.6-x86_64.egg/astropy/config/packagename.cfg: No such file or directory
```

This requires either adapting the configuration file generation so that it works in the package template, or disabling the configuration file generation for package templates. I think we want to allow affiliated packages to use configuration items, so I think the former is needed. I will try digging into this a little, but I think it would be a great help if @eteq or @iguananaut could also look into it, since they are more familiar with this code than I.