How to help or change things or add features
Look at the Wiki, it should have some documentation on how this works, and the structure of each packet/command.
If you want to work on backend features
Most of what you want is in
Database.java, but if you want to fix the IP range whitelisting to support IPv6, that is in the core folder
I recommend eclipse or inteliJ for Java development. Please do not try and push IDE specific files.
If you want to work on frontend features
All webdev files are in the root of the directory. I recommend something like VSCode or Atom for web development (tip: you can open an entire folder with atleast VSCode for easy switching between files)