Great to see a new person on board. I would highly recommend getting a ZNC bouncer account (someone on the board may have one to give) so you can hang out in the dev IRC and catch up with what's going on even when offline for a while. Lots of great advice in there, and they can help you answer those kinds of questions there and then.
If you have got some code (not database) changes that deviate from live, what you could do is create a fork from the main EQEmu source into which you add the more "vanilla" changes. Then create a separate branch off that for your more custom code.
You can them merge changes from the main project to your main fork to keep up to date, and if you want those changes reflected in the more "custom" part then you can merge changes up to that branch too. The key here is that you would never merge changes from your "custom" branch to any of the others.
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