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This is all about a format for packaging your modifications that will make them easy to install by end-users. The QMOD system is basically a rip-off of a similar idea used by the game Unreal – users are given a single file that contains the modification and some metadata; when they open this file, the game interprets the metadata and presents a set-up routine specific to that mod but using the game's standard user interface.
As far as the user is concerned, installing mods for the game will be easy, with a guaranteed user interface and level of accessibility. They also get to choose which mod to play, from a list of installed ones, via the launcher. Finally, they can also uninstall mods easily, again via the launcher.
For the developer, you get the benefit of giving your users the above benefits with very little work – simply package your mod up in the way described here, adding the required metadata! In addition, you can ask the launcher to keep your mod's config files up-to-date with any changes put into the user's standard game config files (at no development cost to yourself).
We've designed this system to make it ideal for people to mod AudioQuake; it does all of the chores of setting up mods for the user and adds little extra work for the developer. There is, however, one situation in which it is not the best way to proceed: total conversions. Total conversions modify the game engine as well as the content and/or gamecode, so they are technically different games.
We felt that those of you making total conversions would want to make your own separate game with its own installer. Naturally, the QMOD system can be used to create mods for any total conversion of AudioQuake, just as it can with AudioQuake itself, so even if you're a total conversion developer, you can still take advantage of it!