Most of the information here is for Warzone 3.1 and above.
Warzone Filesystem
How does the Warzone file system work?
PhysicsFS
When you start a game, Warzone looks in two key places to find it's data:
Application Folder – the core application, data and videos
Config Folder – log files, add-ons (mods, maps, etc), saved games and game settings
Warzone uses the contents of those folders to create it's virtual file system. It does this using a library called PhysicsFS with a few custom extensions.
Understanding the virtual file system is critical if you want to mod Warzone...
What's the "right way" to mod Warzone?
To apply a mod to Warzone, even if you want to change something in the Application Folder, you should create a mod that lives in either the maps or autoload folder as shown below:
<Config Folder> ← How do I find it?
maps ← How do I install a Map? or How do I make a map?
mods ← mods in this folder need to be loaded using command line parameters
autoload ← mods in this folder will be loaded automatically
If your mod contains a map designed for skirmish, challenge or multiplayer games, it should go in the maps folder, even if it has other customisations (such as graphics mods, etc).
All other mods should go in the autoload folder (assuming you want them to load automatically). There are a few scenarios where this doesn't apply, but they're beyond the scope of this intro to the Warzone Filesystem.
What happens when a mod loads?
When a mod gets loaded, it changes the contents of the Warzone file system:
If it contains folders and/or files that don't already exist, they are added to the file system
If it contains folders that already exist, the existing folders are kept (so if there's a folder with files in, you can't empty that folder by putting an empty folder in your mod)
If it contains files that already exist, in the same folder path, the files in the mod will replace them
What order are mods applied in?
To answer this question, you need to know all the key stages of how the Warzone file system is initialised from the moment you load Warzone to the point where a game starts.
First, familiarise yourself with the contents of the Application Folder – opening it in a new browser tab or window so you can refer to it might help.
If you imagine the Warzone file system to be like a virtual hard disk, the data folder is the disk drive:
data → Warzone
Stage 1 - Warzone loads
When you load Warzone, it's virtual disk initially looks like this:
Warzone ← (the data folder)
The Warzone Zip (.wz) files listed above are just like mods, but special ones that come with the game and live in its data folder.
Before the main menu is displayed Warzone "virtually unarchives" the contents of base.wz in to the root of the Warzone drive, which is good because things like menu backgrounds and music live in base.wz.
Now we've got something like this:
Warzone
If sequences.wz is present, it virtually unarchives that in to the root of the Warzone disk as well so all the extra videos are available. Imagine it virtually clicking the "replace all" button if asked to overwrite existing files of the same name.
Next, it replaces the mods folder with the folder of the same name, if found, from the Config Folder:
<Config Folder>/mods → Warzone/mods
If you've got mods that require manual activation (they live in the mods folder, not mods/autoload) and have used command line options to activate some of them, those will be virtually unarchived, in the order specified by the command line options, to the root of the Warzone disk, again with a virtual click of the "replace all" button.