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1. IDE is up to you. Flexbuilder will be required if you are going to do a lot of work with flex UI. Besides Flex, EM plug-ins require a lot of XML editing, so a good XML editor is highly recommended.
2. Yes, we require a specific folder structure. This is covered in the documentation.
3. 'empdk validate_plugin' will validate the integrity of the metadata, but to test the plug-in you have to deploy it to EM and start using it.
4. Java artifacts can only be included on the agent side. So you can call jars or classes from jobs or from fetchlets.