As far as you making some adjustments to the game, you can't call this project clean or stable. This would happen only on the NCSoft's case.
Especially when you're using java. I'm not any guru on this themes, but it's okay. You can do your job with those files too.
Although, stability has too many ramifications which need to be mentioned, in order to give a well balanced end product to lineage 2 players.
By reading those features, i'm pretty covered, but if you're going to open a low rate server with some facilities, make sure they won't affect the original gameplay that have been developed.