Best practice for adding program path for programs intended for compiling

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My software for data analysis has grown to a fairly big size, and is split to several subdirectories,
like /MATLAB/Myprogram, /MATLAB/Myprogram/GUI
and some others. Normally, I just list the paths to startup.m,
and so on. This works fine, but when I compile the software (to be used with MRE), a bunch of warnings are created,
as this is considered bad programming practice for programs intended for compiling (I agree with that). However, the problem is that I HAVE NOT FOUND AN OBVIOUS ALTERNATIVE WAY of telling MATLAB where to find the functions and classes!
What would that be?

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