Afterbirth+ and Repentance come with an unpacker program that will unpack all of the files in the "packed" directory. This is called the "Resource Extractor". If you want, you can run it and your resources directory will fill up with all kinds of stuff. Afterwards, you can examine and replace individual game assets. By default, the unpacker is located at:
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C:\Program Files (x86)\Steam\steamapps\common\The Binding of Isaac Rebirth\tools\ResourceExtractor\ResourceExtractor.exe
After unpacking everything, if you edit or overwrite any custom game assets, they will permanently take effect. However, this will ONLY work if you rename the "packed" directory to something else, as the packed files take priority.
Note that if a mod is enabled in the in-game "Mods" menu, and it has a resource file of the same name, it will overwrite what is in this directory.
Also note that every time after Nicalis patches the game, you should nuke all of the unpacked files and redo this entire process from scratch, or else you will be playing on game files meant for a previous patch.
C:\Program Files (x86)\Steam\steamapps\common\The Binding of Isaac Rebirth\resources-dlc3
This is similar to the "resources" directory, but it contains the files for Repentance. If a file is present in the "resources-dlc3" directory, it will take precedence over the same file in the "resources" directory.
C:\Users\[username]\Documents\My Games\Binding of Isaac Repentance
The "[username]" above refers to your Windows username.
This folder contains the "log.txt" file, which is used by certain programs such as the Rebirth Item Tracker.
This folder also contains the "inputconfigs.dat" file, which contains all your key bindings. (It is just a text file, so you can open it in Notepad to edit it if you want.)
This folder also contains the "options.ini" file, which contains some values that you can set using the in-game menus. (This is also just a text file, so you can open it in Notepad to edit it if you want.)
The "options.ini" file also contains some values that are NOT in the in-game menu. One such value is "SteamCloud". By default, it will have "SteamCloud=1".
If "SteamCloud" is set to 1, the game will look for save data from the Steam save data directory, listed below as #5.
If "SteamCloud" is set to 0, the game will look for save data from the same directory that the "options.ini" file is in (the "Documents" save data directory).
The "[Steam ID]" above refers to your Steam ID number. If you don't know it, just look inside the "userdata" directory, as there will probably only be one subdirectory there.
C:\Program Files (x86)\Steam\steamapps\common\The Binding of Isaac Rebirth\mods
This contains directories for each Steam Workshop mod that is installed.
Mods that appear in the in-game "Mods" menu will correspond to the directories here.
By clicking on the "Subscribe" button on a mod's Steam Workshop page, the respective mod will automatically get downloaded here (and be turned on the next time you launch the game).
This is where mods from the Steam Workshop get downloaded to before they are sent to the "real" mods directory.
If you are unsubscribing from a mod for the purposes of redownloading it from Steam, you must also delete this directory in order to force a true redownload. Otherwise, Steam will just copy the mod from its cached directory.
Either way is fine, but we recommend that you turn it off, since it will prevent your save files from accidentally being deleted in case Steam messes up. Also, it becomes easier to manage your save files, since they will just exist in the same directory as everything else (options.ini, log.txt, and so on).
If you do not use SteamCloud, folder #4 will contain the files:
persistentgamedata1.dat
persistentgamedata2.dat
persistentgamedata3.dat
If you use SteamCloud, folder #5 will contain the files:
rep_persistentgamedata1.dat
rep_persistentgamedata2.dat
rep_persistentgamedata3.dat
These correspond to save file slots 1, 2, and 3 respectively. If an in-game save slot is blank, the corresponding ".dat" file may not exist.
Furthermore, each save file slot may have a corresponding ".dat" file that contains the status of the current run, so that it may be resumed by the "Continue" feature. These files are called:
gamestate1.dat
gamestate2.dat
gamestate3.dat
Furthermore, the game occasionally makes backups of the various save files. It will prepend the date to the name of the save file. For example, this is the name of a slot 1 save file backed up on January 15th, 2017: