There is a difference between testbench files and simulation files:
Testbench files are independent of the simulator and comparable tools. They include testbench configuration files, test case descriptions or stimuli and golden reference output files.
Simulation files are setup and command files for a simulator or similar vendor tool. Related configuration files include waveform settings and simulation scripts.
A project’s folder structure should also draw this distinction to keep simulator/vendor independent files separate. Log files and results should therefor be put in an output folder alongside the testbench files.