Directory Structure

Not all files/directories might be available, depending on your setup

Linux

<MultiMC root>
├── accounts
│   └── skins
│       └── <username>.png
├── accounts.json
├── assets
│   ├── indexes
│   │   ├── <version>.json
│   │   └── legacy.json
│   ├── objects
│   │   ├── 00
│   │   │   ├── 000<some more stuff here>
│   │   │   ├── ...
│   │   │   └── 00F<some more stuff here>
│   │   ├── ...
│   │   └── ff
│   └── virtual
│       └── legacy
├── cache
├── iconengines
│   └── <libraries>
├── icons
├── iconthemes
│   └── custom
├── imageformats
│   └── <libraries>
├── instances
│   ├── instgroups.json
│   ├── LiteLoader 1.7.2
│   │   ├── instance.cfg
│   │   ├── minecraft
│   │   ├── patches
│   │   │   └── com.mumfrey.liteloader.json
│   │   └── version.json
│   ├── Forge 1.6.4
│   │   ├── instance.cfg
│   │   ├── minecraft
│   │   ├── patches
│   │   │   └── net.minecraftforge.json
│   │   └── version.json
│   ├── Vanilla 1.5.2
│   │   ├── instance.cfg
│   │   ├── instMods
│   │   └── minecraft
│   └── Vanilla 1.7.2
│       ├── instance.cfg
│       ├── minecraft
│       └── version.json
├── jars
│   ├── JavaCheck.jar
│   └── NewLaunch.jar
├── libraries
├── lwjgl
│   └── 2.9.0
│       ├── jinput.jar
│       ├── lwjgl.jar
│       ├── lwjgl_util.jar
│       └── natives
├── meta
│   └── <meta json files>
├── metacache
├── mods
│   ├── minecraftforge
│   │   ├── forge-1.6.4-9.11.1.965-installer.jar
│   │   ├── forge-1.7.2-10.12.0.999-installer.jar
│   │   ├── json
│   │   └── list.json
│   └── liteloader
│       └── versions.json
├── MultiMC(.exe)
├── MultiMC-0.log
├── MultiMC-1.log
├── MultiMC-2.log
├── MultiMC-3.log
├── MultiMC-4.log
├── multimc.cfg
├── notifications.json
├── platforms
│   └── <Qt libraries>
├── qt.conf
├── styles
│   └── <Qt libraries>
├── themes
│   └── custom
│       ├── resources
│       │   └── <theme assets>
│       ├── theme.json
│       └── themeStyle.css
├── translations
│   └── mmc_de.qm
└── update
    └── backup

Explanation

File/Directory	Description
accounts.json	All your accounts are saved here. No passwords are saved here, though the different tokens could be used to play Minecraft as you, so be careful
assets/indexes/	The files here contain information about the assets for different versions of the game, like which asset ID belongs to which asset.
assets/objects/	All "new" assets are stored here. They all have a 40 letter hexadecimal ID, and are sorted into folders according to their first 2 letters.
assets/virtual/legacy/	Assets for older versions of Minecraft
cache/	Various downloaded files for the different modpack platforms
icons/	All custom icons you give to MultiMC are stored here
iconthemes/custom/	Custom Icon theme for you to edit, see Custom Icons for more information.
instances/instgroups.json	This file defines in which groups the instances are sorted
instances/<instance>/instance.cfg	This file keeps all the instance settings, such as memory options, as well as it's name etc.
instances/<instance>/version.json	1.6+ ONLY: This file contains all the information needed to launch a vanilla instance, like libraries needed etc.
instances/<instance>/custom.json	1.6+ ONLY, DEPRECATED: Like version.json, but for usage in modded scenarios. Can be used for completely overriding version.json, but it's recommended to use [patches](JSON Patches) instead
instances/<instance>/minecraft/	This is the "normal" Minecraft directory, which contains, saves/, mods/ etc.
instances/<instance>/instMods/	Pre-1.6 ONLY: The directory containing jarmods
jars/	Since MultiMC isn't a Java program we use a few different Java applications for things like launching the game. Those are stored here.
libraries/	This contains all of Minecrafts dependencies, see below for more info
metacache	This file contains information about most downloaded files and is used for keeping track of them and making sure they are always up-to-date
meta/	Downloaded cache files for the previously mentioned metacache
mods/minecraftforge/*.jar	Forge installers
mods/minecraftforge/json	Local copy of the Forge version list (gradle generation)
mods/minecraftforge/list.json	Local copy of the Forge version list (pre-gradle generation)
mods/liteloader/versions.json	Local copy of the LiteLoader version list
MultiMC	LINUX AND OSX: This is the main executable, but it should never be called directly. Always use the script at root
MultiMC.exe	WINDOWS ONLY: This is the main executable.
MultiMC-*.log	MultiMC logs, the logs of the five last launches are kept
multimc.cfg	MultiMC global settings
notifications.json	Local copy of the notifications list
platforms/	Needed by Qt
plugins/	Needed by Qt
qt.conf	Needed by Qt
styles/	WINDOWS ONLY: Needed by Qt
themes/custom/	User-editable custom MultiMC theme
translations/mmc_<lang>.qm	Translations of MultiMC, Translating MultiMC for more info
update/backup/	Backup of the MultiMC binary for the updater