How can I add custom week numbers to Calendar?
I do not know of any way of customising the existing function, so I suggest that you make an iCloud Calendar and make a repeated calendar entry for each semester. Example: Make new calendar named Semesters. Make an entry called 201516-1 and set the first Monday of the semester and repeat until the last. Continue making entries 201516-2, 201516-3, 201516-4 until you are done.