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Im also working with flex. Regarding folder management, You can make comfortable for you. .as files shall be placed at any folder. I donno about coldfusion. But im using java for business logic, in my case im using jrun server, there i can place my root folder within " Default" folder.I should copy and paste "WEB-INF" folder from "samples folder to my root folder, in order to deploy my folder. Except the webservices(may be java class file or jsp) files i shall place any other files within my folder structure. In case of class files, i should place those inside "WEB-INF\classes\" folder. This may be helpful to you.
There is also called
1] virtual directories, and
2] Linked Resources
Virtual directories map a request path to a real path in your file system. You can keep your files in directories outside of the application directory structure, but map them to a path inside the application directory structure.
For example, you can store files in an images folder at C:/images/production and use those images in your applications by adding a virtual directory that points to the /flex/images/production folder.
Linked resources are files and folders that are stored in locations in the file system outside of the project's location. These special resources must have a project as their parent resource. Linked folders and files can be used to add resources to your project that for some reason must be stored in a certain place outside of your project. For example, a linked folder can be used to store build output separately from your source files.
You can even use linked resources to overlap other resources in the workspace, so resources from one project can appear in another project. If you do want to have overlapping resources in your workspace, do so with caution. Keep in mind that this means changing a resource in one place will cause simultaneous changes in the duplicate resource. Deleting one duplicate resource will delete both!