Remember certain layer settings
One of the main time wasters I've encountered is the fact that Phoenix does not individually remember selections I had made in different layers.
Imagine you have a Matte Paint and a DVO Fix layer. I use the Matte Paint layer to paint out false positives from DVO Dry Clean, let's say, and I use DVO Fix to clean any remaining defects.
As I'm evaluating the frame, I constantly go back and forth between these two layers, which I can hotkey for speed, but in Matte Paint, I'm always using a Rect to draw, whereas in DVO Fix, I always use a brush. So, as I switch between layers, I constantly have to re-select Brush and Rect, respectively, because Phoenix only keeps track of the "current" selection.
It would be so much better if it kept track of the selection per (sub)layer so that whenever I select the DVO Fix layer, it automatically switches to brush mode, and when I go to my Matte Paint sub-layer, it switches to the Rect mode again.
There are a few other parameters as well that would benefit from being tracked on a per-layer basis, depending on the effect.
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It also applies to DVO Fix in general. Because I cannot mix "Auto Fix" and "Clone" mode in the same frame, I usually have two DVO Fix layers, one for Auto Fixes, one for Clone fixes. However, when I switch between these layers, I constantly have to adjust the fix mode by hand as well, because it just doesn't stick.
It would save so much time if the layer itself would remember whether it was set to "Auto Fix" or "Clone" mode and automatically switch back to it as I switch between these separate DVO Fix effect layers.
Or even better yet, allow mixing Auto and Clone mode within a single frame so I don't need two layers to begin with, and then hotkey the mode. Now that would be a super-useful timesaver!