The phrase "to run in" means to gradually introduce something new into a system or routine, often by starting with small amounts and gradually increasing until it becomes fully integrated. It is commonly used when referring to equipment or machinery that needs to be tested and adjusted before being put into full operation. For example, if you were to say "The new car engine needs time to run in," what you mean is that the engine needs to be driven for a while so that all of its parts can wear in and become fully functional.