Add in an option for preserveAll

I added this in because of the following scenario...

I have a temp folder in a project.

```
/templates/
/templates/view.js
/templates/view.amd.js
/templates/router.js
/templates/router.amd.js
...
```

The *.amd* version imports the non-amd version, however I still wanted the non-amd file to be included. I knew that all of my templates were going to need this, so the preserveAll option seemed to be a good way to allow this behavior.

Thanks!