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Good APIs are hard to design. Mojang has stated that their API was intended to be better than Bukkit. Since Bukkit was already pretty good, they would need to - and have been - putting a lot of work into it. On top of that, they started with a rather large established codebase, so most of their API effort has been preparing Minecraft for the API, which has had less immediately obvious results, except perhaps to those actually digging through decompiled Minecraft code.
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There was nothing about the DMCA notices for Mojang to comply with. A DMCA notice demands that certain files are immediately removed, the only option is to file a counter-notice. If the the site hosting the files did not comply, they would no longer be protected from the copyright infringement of all user-uploaded content.
While the entire thing could be seen as someone trying to force Mojang to open-source Minecraft (the only way I see Mojang even being given a choice that they could have “complied” with), that assumes that the change would retroactively make it valid for all contributions, something I would not rely on without consulting a lawyer (Mojang likely consulted a lawyer). -
Mojang profited off the “hundreds of talented developers” exactly as much as if they hadn’t bought Bukkit. Code was licensed to the Bukkit project under GPL/LGPL, the actual right to the code was not transferred (no CLA), unless Mojang made private deals with specific individuals (which could have happened even if Mojang had not bought Bukkit). Mojang would have profited indirectly, though increased Minecraft sales due to increased popularity from the success of large servers, some of which was made possibly by Bukkit, and all of which would have occurred regardless of the owner of Bukkit (unless the owner decided to stop the project early).
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