Currently, of all the IDEs, FDT probably has the best built-in support for FlexJS.

They have an easy-to-follow guide to using FDT with FlexJS on their blog. The walk-though is with version 0.5.0, but adding later versions is a simple matter of selecting a FlexJS SDK as a Flex SDK. FDT will automatically recognize it as a FlexJS SDK and will allow compiling to Javascript.

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