Since version 1.2.1 Alloy is throwing errors like:
Script Error Couldn't find module: alloy/widgets/sc.Weather/controllers/widget
When I check the Resources directory, not all widgets have been compiled and copied to the Resources directory.
I created a test app, where I created 2 Widgets using the New -> Alloy Widget menu shortcut and added them to the index controller:
The widgets are completely left untouched, so is all other code except for the index controller.
Downgrading to Alloy 1.2.0 solves the issue.
The test app can be found here: https://dl.dropboxusercontent.com/u/1849335/AppcJira/tv.wappzapp.alloy121test.zip