On the CS50 info page I have read that certifications will be generated on June/September 2014, does that mean if I haven't finished all the problem sets and final project before September I won't be able to receive a honor code certification?


No, those are simply some extra dates for folks who have finished by then and don't want to have to wait until after 31 December to get their certificates. The final deadline for the course is 31 December 2014, so you need to have finished by that date.

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