First of all you need to understand that there is no ultimate guide "how to", server sources has some similar things but it also has some differences that you will be hard to adapt without skills. Saying skills I mean not only java skills, the most required ones is understanding lineage 2 core processes task-scheduling and client-server networking communication.
You need to:
-learn some core information about Java language
-learn some lessons about java programming to understand what is java classes, packages, imports etc.
-learn how to edit java source code with some IDE (one of them eclipse)
-learn how to compile java source code (with ant for example)
Then for the best way you need to get most popular sources form thread above and try to integrate that scripts like for native, I mean as I can see that mostly provided scripts are for acis, so take acis sources and ty to integrate or find something directly for mobius etc.
Doing all this you will need to understand three things
First - How player communicates with server
What is action bypasses (when player clicks some link in HTML) and where your server handles it (find RequestBypassToServer packet and learn how its working)
What is user/voice/admin commands (when player writes some in chat with "." or "/" or "//") and where your server handles it (find VoiceCommandHandler and learn how its working)
Second - How server doing core logic
If addon has some logic that not depends on direct user action it will mostly required some scheduled task (some logic that will be runs periodically), so you need to find some ThreadPoolManager and Runnable usages and understand how its working
Maybe you will need some data storage, so you will need to find how server working with database (try to find how server executes SQL requests, SELECT, INSERT, UPDATE)
Third - How server communicates back to player
You need to find how server sends packets to player, find some sendPacket() method and its usages, for example Say2 packet (its when server sends some chat message to client) etc
Unfortunately there is no easy way, some sources will be easier to adapt cuz of similarity between sources some will be harder