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@anthony - glad you are finding the plugin useful.
As for the ability to run multiple checks at once, yeah it has been a little discussed a few times in this thread. It is on my "maybe one day" list. The problem is coming up with a way to present the results to the user that is useful. The key difference between this plugin and Modify ePub is that with this plugin you need the set of books found from the check to then perform the bulk edit/Modify ePub or whatever operation to "fix" the issue you were looking for. When you start allowing multiple checks to run at once, all of which could have unique, duplicate or intersecting sets of results of books, it adds a problem of how to work with the results.
The only thing that comes to mind is to have some sort of modeless results summary window that shows one summary line per check ran, and then as you click on that line it displays the matching books in your library view so you can do your work on them. Then you click on another summary line and it shows those books etc. When you add in a new dialog allowing the user to select which checks to run it becomes a non-trivial exercise.
I have no doubt it will happen one day, but only when I feel a bit more enthused about investing more time in calibre plugins...
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