I thought I recognized this word, so I checked up on it:
I'm only learning, so I'm not sure of my answer, but I would guess it is to mark the difference from "that fork" ("o çatal")
I am learning as well. I am sure that the comma is there to make clear that the meaning of "O" is "he,she,it" and not "that". It is only to avoid misunderstandings in written language.
No. "yer" is aorist (roughly, simple present) tense -- the imperative form would be "ye" without the -r.
"O" means "he" or "she" or "it".
You can often leave it out since the verb ending in "yer" (or rather, the absence of a personal ending, in this case) shows that the subject must be "he/she/it".
"O, bir çatal ile yer." = "Bir çatal ile yer." = "He/She/It eats with a fork."