If you really need to combine disparate sets of code into one project, the most obvious approach is to design your overall hierarchy and have each set of generated code connected to the appropriate others via a handwritten top level wrapper.
Beyond this, HDL Coder has the capability to combine code within its framework. You can include arbitrary code at an arbitrary location using the black box functionality. This code can be hand written or, it can be generated by HDL Coder, or by any other tool.
If the code was generated from a separate Simulink model, you can consider using a model reference block to reference the other model in Simulink and to generate HDL code for the combined design at the same time. HDL Coder also allows the embedding of System Generator subsystems within it.
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