Afterbirth+ comes with a plethora of modding tools for you to use, including 5 utilities and a LUA API, which allows you to add items and enemies and many other things to the game via LUA scripts. You can find these files in the tools folder of your Rebirth installation.
Getting Started / Resource Extractor
One of the first steps to begin Afterbirth+ modding is to get a dump of all of the game's resources, which are stored in the .a files. To do this, right click on Rebirth in your library, hit Properties, then Local Files, then Browse Local Files.
In this folder will be a folder named tools. This folder contains all of Afterbirth+'s mod tools, including the documentation, mod uploader, resource extractor, room editor, and more. For now, we're interested in the resource extractor, so double click on that folder.
The resource extractor is a command-line tool. On Windows you can double-click the .exe and a command prompt will come up and guide you through the process. On Unix-based systems (Mac and Linux) you'll need to open a separate terminal in the folder and run the resource extractor from there by running "./resource_extractor". This process will extract all of the game files in to the resources directory.
If the game updates, it is recommended to repeat this process in order to ensure you have the most up to date files. As of the Jaunary 7th patch to Afterbirth+, the game no longer loads these unpacked files by default, so it is only necessary to update your unpacked files if you're using a modified version of these files in a mod.
The Room Editor allows you to edit the layouts found on the floors in the game. You can edit or create new layouts, letting you change everything from generic enemy rooms to item rooms and curse rooms. All entities are available, so you can add items, pickups, enemies, bosses, and other obstacles into your rooms.
The Animation Editor allows you to edit the animations of all entities. For example, you can change a boss's attack animation, or an enemy's walking animation.
Item Pool Editor
The Item Pool editor lets you change what items you will find in different areas of the game. The game divides discoverable items into different categories based on where you are in the game. You will want to use this to add or remove items from different pools.
This tool lets you upload your mod to the Steam Workshop. Choose and title your mod, set the tags and other information, and hit upload mod. Easy!
The Lua API allows you to make more extensive changes to the game. You could technically change the game into another game entirely!
The Lua documentation is available in your tools folder, however we also host the documentation here on Modding of Isaac for easy access and linking purposes.