1. A computer-based file comparison system for comparing annotations within files comprising: a processor; and a memory coupled to the processor, the memory storing instructions to direct the processor to perform operations comprising: receiving a first file and a second file for comparison, determining a first annotation range for a first annotation in the first file, determining a second annotation range for a second annotation in the second file, determining that the first annotation range and the second annotation range overlap, and comparing the first annotation and the second annotation to create an annotation comparison output that includes compared annotation text representing differences between text in the first annotation and text in the second annotation.