Add support for generating wrappers for files in subdirectories.

Also removed dart files when there are no polymer elements being wrapped.
here it probably doesn't matter, but we try to avoid + if possible and either use StringBuffer or interpolations if possible. In this case one option is to do:
```
var linkTags = ...
var scriptTags = '';
if (hasDartFile) {
  scriptTags = '<....>';
}
...
writeAsStringSync('$linkTags$scriptTags');