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Originally Posted by MP2 My main 'concern' is this: I create a function, for example, CreateDoubleRainbow(), and it's in some file in my server files, for example /scripts/core/objects/blah/dir/lol/rainbows.inc

That is the main problem (I mean I won't even hide my p*rn files in that many sub-folders). You have taken the "using many include files" too literally. Don't use a new include for each and every function you create, that's just a mess (according to me). Try to use a different include file for a specific system, for example, if you're creating a weather changing system, use a specific include for that which contains all the functions related to weather changing only. This is one way. You can store them include/systems/*.inc

The other way, is to use a different include for every type of code (this can get a bit messy). I cannot express myself but what I mean is to make a specific include containing all the functions, a specific include for all the variables, for all the macros, defines etc. You can store them as include/*.inc

Using one of these methods, you know where something is. You're concerned with changing a part of the code in your weather changing system, you look for it in the 'weather.inc' or if you want to change a function, you search the 'functions.inc' rather than searching for it in multiple directories.