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I guess I just don't see the issue. You have to download and install all of calibre to use any of these addons, so why would it be such a hardship for someone to use the main gui to install these addons? It's just the one time (per plugin) and then you can go back to ignoring main program if you like.
It's no real skin off my nose either way, but it just seems sort of pointless to me to focus on plugin framework isolation when the various pieces (library, converter, viewer, editor) share way too many resource to ever be truly independent of each other anyway. Not to mention the inefficiency of maintaining separate plugin frameworks from a code-base perspective.
The way I figure it: if you just want to just use some of calibre's features independently ... have at it. But when it comes time to extend those features with third party tools ... it's not that outrageous that we're expected to return to "home base" to do so. *shrug*
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