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In Flex Builder you can change in the project properties in the Flex Builder Path the Main Source Folder allowing to set up the root folder wherever you want.
Thanks for your response.
So essentially you can't choose an application file that is not in the root folder? That doesn't seem very flex ible...
Sure you can change it, but you'll have the modified the app settings as I told you.
You are saying that you can change the source root of a project, and that's fine, I know that. But that isn't answering my question - if you can choose an application that is NOT in the project root folder...
One reason I don't want to change source root is that I want to maintain fully qualified package names. Compare with a Java project for example, you wouldn't want to set source root in the middle of your package structure...
Perhaps I can setup multiple source folders in Flex Builder...
Anyhow, my build script does what I want.