>>Anyway, what I haven't been able to figure out is how to make the command window not always be on top. I tried checking the context menu, but there doesn't seem to be anything there. I also gave a rather quick look at the Options dialog, but there didn't seem to be anything there either.
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>Right click the titlebar and turn off dockable.

This may seem rather "thick", but what's dockable (other than always on top) supposed to mean? My instinctive reaction was that it meant that you could dock the command window on the tool bar and drop it down like you can do with the project manager in previous versions. I thought that might be pretty cool. But that's not the case.