In the free software world, compiling programs from source is commonplace. As you might expect, the vast majority of programs don't ship configured by default to use the GoboLinux directory hierarchy... though most are quite happy to use it. Those that aren't can be persuaded -- as a last resort, there's always the compatibility "legacy" directories. Most of the time, you won't have to deal with it, though: compilation rules for hundreds of programs are already automated in the Compile program and its "recipes" tree.

Search recipes in the Recipes repository.

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