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Protobufs
protobufs are one of man's most important means of passing information around. Via CMake and co, the .proto files storied in share/messages are semi-automatically compiled when you build man. To (re)compile their java equivalents for nbtool, run GENERATEproto. This will search share/messages for .proto files and protoc them into the appropriate place for building with nbtool.
This is not automatically done when RUNnbtool or BUILDnbtool is executed.