Add support for generating wrappers for files in subdirectories.

Also removed dart files when there are no polymer elements being wrapped.
maybe move the first 2 ../../ to the packageLibDir definition above? I wonder if that logic can be simplified a bit, but I'm not sure yet. The whole distinction based on the number of segments is a bit tricky. Maybe something like:
```
var inSubdir = segments.length > 4;
var packageLibDir = '../' * (inSubdir ? (segments.length - 1) : 2)
```