0 - Introduction
ModCS is a Cave Story modding utility, which's main feature is Lua Scripting.
This modding guide will go over the basics of Cave Story modding before going into scripting. Although this guide's main purpose was for ModCS, it will contain extra information about differences in modding between different engines, so if you are new to modding this guide may be a good introduction for any type of engine (Original Freeware EXE, CSE2, etc.) until the Scripting Section, which will exclusively focus on ModCS's Lua Scripting.
If you are having any trouble with anything unrelated to Lua scripting there are a couple of places you may ask for help, such as the Cave Story Modding Community or the Cave Story Tribute Site Forums.