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#6 snapshot window level can obscure prefs window
If you have a bunch of snapshot windows around, clicking the 'keep snapshot windows on top' pref can cause them all to pop above the prefs window, and make it difficult to get back to.
Perhaps the prefs window should be at a higher level?
Also, perhaps the snapshot windows should be at a lower level. Should they really be shown above windows in other apps?
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A pref window is usually a normal window, not a utility window, so usually it should not be in the floating window level.
The snapshot windows are only in the floating window level in fullscreen mode and when you choose this in the prefs. The default is to have them in the normal window level. It can be useful to have them on top, that's why I added the pref. Also, when they are on top, they are hidden when skim is not active.
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Ok, I'm just going to avoid using that pref, since it annoys me (a little) how the snapshot windows can completely block other regular windows if they're large. I can't think of a good way to fix it for everyone...