I LOVE THIS.
I imagine the experience playing out like this:
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Thread Entanglement is a toggle in a user's settings menu.
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The comments section of an entangled thread merges all comments from every iteration of the thread entangled. Each comment would have some indication of which entangled community it actually belongs to. Replying to a comment will of course federate your reply to that community's thread.
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Posting a new top-level comment offers something like a drop-down box to determine which community a user specifically wishes to affiliate that comment with, but could otherwise default to the local-most, earliest, most populated iteration of the thread, or even a general hashtagged post -depending on user settings.
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A community filter/toggle within an entangled thread would allow users to instantly remove all comments from one or more communities.
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Communities blocked or not subscribed to by a user will of course not appear in entangled threads unless directed to do so in settings.
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Entanglement-exemption options in a user's settings menu could include which communities or users to omit from entanglement, or if any specific communities should be omitted from consideration when posting a new comment in an entangled thread.