I think it was the immigrant burglar named Rudy Guede who had a history of breaking into second story buildings by smashing the window with a rock and climbing on in. The cottage had a broken second story window smashed open with a rock. His various criminal activities, aside from burglary and trespassing, also included knife wielding. The victim was stabbed to death. His DNA was found in the victim's gentitals and he left his handprint in her blood, and footprints matching his shoes made in the victim's blood were found around the body and trailing away from the crime scene.
The victim's state of digestion, taking into account the start time of her last meal, strongly suggested she died not long after she arrived back at the cottage which was 9 PM local time. Meredith was known to be attacked while still wearing her outdoor jacket. Her cell phone had unusual activity by 10 PM local time suggesting it was no longer in her possession. All of this supports Rudy's own testimony, which is that she was almost certainly dead by 9:30 PM local time, which alibis the students Amanda and Raffaele, not that any evidence or plausible theory would tie them to her death. But this is just my opinion. You may have a different one, which is more wrong and less based on the facts.