update to always write QIIME config file

qiime-deploy now writes a QIIME config file under the deploy dir, even if there is no QIIME target in the conf file. This is necessary since we will be removing QIIME and most of the other python dependencies from qiime-deploy, but we still want a QIIME config file created.

It is now possible to do:

```
pip install numpy==1.7.1
pip install qiime
python qiime-deploy.py ...
```

and get a fully functioning QIIME installation.

Related to, but doesn't completely solve, #55. Still need the qiime-deploy-conf repo updated to fully resolve the issue.

This is ready for review/merge, and should continue to function with the existing qiime-deploy-conf files, so that users can continue to install QIIME 1.8.0 using the current method.

@gregcaporaso or @antgonza can you please review?