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I've been using PI for a little while now too and as you've already mentioned it the workflow is a little odd at first with the processes hierarchy. It takes a little getting used too. It has some powerful tools but I still use CCD Stack and Photoshop extensively. My favourite noise reduction is still Noiseware Professional by Imagenomic. I've used Noise Ninja, PS native noise reduction, NeatImage, PI ACDNR. Maybe I'm using them wrongly but I never got a better result than using Noiseware with very small incremental passes.
I love PI DBE. It does a great job at salvaging pictures plagued by gradients. Gradient exterminator still has its place in my bag of tools though as it is easier to use. I also like HLVG in PS to get rid of green casts. PS is also THE application to blend layers. I know the PI purists make a point to say painting is a crime but I still use that a lot: layering, masking, etc... It's easier and more intuitive than using PI masks and clone viewports.
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