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These chunks are unfinished, and waste cpu time saving these unfinished chunks. the loadChunk method refuses to acknoledge they exists, and will restart a new chunk generation process to begin with, so saving them serves no benefit.
Paper 
High performance Spigot fork that aims to fix gameplay and mechanics inconsistencies.
IRC Support and Project Discussion
Documentation
Access the Paper docs here: paper.readthedocs.io
Access the Paper API javadocs here: destroystokyo.com/javadocs
How To (Server Admins)
Paperclip is a jar file that you can download and run just like a normal jar file.
Download a copy of paperclip.jar from our build server, here.
Run the Paperclip jar directly from your server. Just like old times
Paper requires Java 8 or above.
How To (Compiling Jar From Source)
To compile Paper, you need JDK 8, maven, and an internet connection.
Clone this repo, run ./paper jar from bash, get files.
How To (Pull Request)
See Contributing
Special Thanks To:
YourKit, makers of the outstanding java profiler, support open source projects of all kinds with their full featured Java and .NET application profilers. We thank them for granting Paper an OSS license so that we can make our software the best it can be.