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Libraries should be stored in a platform-specific folder and referenced in the project using platform-specific variables or macros. For example, on Windows, libraries could be stored in a "lib" folder and referenced using the LIBRARYPATH variable, while on Linux, libraries could be stored in a "lib64" folder and referenced using the LDLIBRARY_PATH variable. Alternatively, libraries can be packaged with the application itself, eliminating the need for the user to install additional dependencies.