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So a few days with impact engine and I am getting comfortable with it for the most part but occasionally I am like where does the code for this concept belong?
I took what I know from the

so when I clean it all up here is what I use mostly

server.bat - executes server js
server.js - server side socket
index.html - client side socket and any html css added by designer.
main.js - key binds, initial spawns, draw updates

entities - player.js - most people have this entity.... key handlers for events
other entities.js - curous what everyone else uses here I have some ideas like extra game menus and a huds and such but its a bit out of the scope of my question

the video I saw kind of broke this organization protocol so I'm curious if im way off on how this should be organized.

Also where can I look for the best way to bring a database (hopefully mySQL) to interact with the game.

How do I keep people from cheating by editing the values in their memory with a hex editor.

There are several options on getting database info and handling cheaters. The more you can do on the server side the better. You can do some on client side but make them run from server side variables. It is kinda a mix.

Use ajax for database inclusion. I will finish my videos