Does the simulation script generated by Tools menu > Generate Simulator Setup Script for IP in Quartus® Prime Pro Edition include the user design files in the project?

Generate Simulator Setup Script for IP generates only the source files and library scripts needed to simulate the IP included in the project. 
User design files are not automatically included and must be added to the generated msim_setup.tcl.

See the article below for instructions on how to use the Generate Simulator Setup Script for IP feature and how to add user designs.

How to functionally simulate a design containing IP generated by Quartus® Prime Pro Edition in ModelSim 

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Category: Simulation 
Tools: Quartus® Prime 
Devices: -