no its not a certificate issue...
it looks like you were going from 1.0.9?
but also then... you were on the master branch for factory, which is not correct for 1.0.9 either.
what version had you used before?
Im a bit confused why you were not at HEAD.
did you have outstanding changes in the community library?
had you changed any of the factory objects?
were you using a 'developer build version?'
IF so did you follow my instructions about removing sub-modules?
had you done any manual git operations?
can I see the earlier part of the console...
as I say, your setup looks like it was in a inconsistent state, to what I would expect axoloti to put you in....
I will say, I think i can make some changes so the upgrade process will use a bit more 'brute force' if users have an 'inconsistent state'.
(e.g. it looks like you don't have contribution details, so therefore I could have just trashed the community and factory folders, and re-downloaded them)