When you import an Alloy project in Appcelerator Studio that was not a Titanium Studio project, it will not get the Alloy nature.
Users who have been using the Titanium CLI will run into this issue when they follow our instructions to migrate their app to the Platform and decide to now use Appcelerator Studio to do so.
1. Create a project through the Titanium CLI (ti create -t app).
2. Initialize it as an Alloy app. (alloy new).
3. Import the app via Appcelerator Studio.
4. Confirm it does not have the Alloy nature.