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1.1 Getting Started [Mod Development]
About the mod loader, and files used
Since Comcraft Mod Loader 0.3 (IDE 0.4) all mod data is stored in a deployable .mod file. These files store all compiled source codes, the mod info (Metadata/Manifest whatever you call it), and all resources in a GZIP compressed format.
More information can be found on Using The IDE next.