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The way I have been using my library has mostly been as a library in a REPL or in small CLI applications, and in those cases the logging output has been tremendously useful to diagnose problems with the files I was working on (mostly region files that got corrupted by missbehaving mods or Forge updates...), so I don't think simply removing the logging calls without replacement would be a good idea.
Overhead should not be a concern, as the actual meaty part (the NBT parsing) has no logging whatsoever, and most logging is only there to notify users of edge cases during de-/encoding of region files.
I definitely agree though that logging should be up to the end developer, and I havn't really taken that into consideration, so I'm gonna see if I can come up with a good replacement for these logging calls, possibly a running tally of these edge case issues that could then be used by said end developer to better inform their own logging decisions.
Reasoning
Btw, your library looks really good otherwise!
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