Wolfram released a new version of their workbench named Workbench 2. It has all the features one can expect from a professional development workbench. Based on Eclipse 3.5 it comes with a Mathematica Debugger, facilities for Unit Testing, Deployment, Refactoring ( quick-fixes as they call it ) and tools for Documenting source. They have published a set of video tutorials
here. With J/Link you can use Mathematica in Java and Java in Mathemica whatever you prefer.
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