If you're using a version of the framework with the old structure (before the release of 0.1), you can convert your project files using this command :
sed -i -f sed_convert_old_structure {file_name}
With {file_name} being the file you want to convert. Wildcards can be used.
You find the sed_convert_old_structure file in /scripts
Remark : The old structure conversion was started before the first beta release. Chances are small you ever used the old structure if you used an official release (0.1 or later).