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...and now I have to eat my words.
Running calibre 5.3 (linux), just updated a plugin and installed a second plugin, then hit the restart button.
Calibre closed its window, waited a few seconds, and popped up the "another calibre is running" dialog. I waited a few more seconds and manually re-ran it and all is good.
So restart is still giving me problems, even when it's highly unlikely to be thrashing.
Irritating, but not a big deal.
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