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Ah, that's an oversight. If I recall correctly there was a time when the initial color grids, the field of many small swatches you see when first pressing a color well before you press More... to move on to a full color picker dialog, included some duplicate groups pre-set with alpha values. That turned out to be a bad idea as initial testers couldn't make heads or tails of them since it is very difficult to indicate which are alpha with such small swatches, and cluttering up the grid with gadgety user interfaces or graphics defeated the purpose of having simple, clear, fast choices from the grid. There were also a variety of new experimental palettes added, which seemed to clutter up the existing lists (already long). Beaded Pastel Alpha was one of them and should have been removed, as it's an outlier compared to all the other non-alpha palettes. I think tastes can reasonably differ in such things but to my taste what is really needed there are two (or three) different approaches. First, it would be convenient to load user-specified palettes into user specified groups besides Classic and CB. Second, it would be convenient to have a few extra palette groups that match, say, other GIS packages like Arc. Third, if you want to globally edit palettes, that's a different thing than a color picker dialog. Manifold doesn't provide a palette creation and editing subsystem, which ends up being a pretty big subsystem if you look at applications for creating palettes and editing them. Instead, there is a context menu in the thematic formatting system in the Style pane: 
That context menu allows making simple adjustments to the selected swath of colors. But that's not a color picker dialog function, even though you could also use a color picker dialog (like Select Color) to lighten or darken. But if you want to introduce *new* features to manipulate palettes, where I'd start would be to add two more entries to that context menu, "More Opacity," and "Less Opacity" [or maybe, "More Opacity" and "More Transparency", or "Opacity +" and "Opacity -"... the usual debates about command names...] and possibly an "Opacity..." entry that pops open a dialog that allows entering a number for percent opacity. (Technically, the internals all use alpha but the UI in Manifold uses percent opacity since that's more comprehensible to more people.) The above is not a palette editing system, but it is a way to get immediately useful ability to specify alpha for more than one color at a time that is being used in thematic formatting. I think next rather than diving into a full palette editing subsystem I'd look into loading user-specified palette files on startup. A problem with that is such initialization steps slow down the initial launch. Every little check, like touching the file system, takes some time and that adds up. The unrestrained "oh, let's put another option into user startup files..." approach to customization you get with some applications is why they take so long to launch. I'd hate to see Manifold lose its very snappy and quick launch.
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