According to Order 66, all Clone Troopers were programmed to kill Jedi on sight. The likely identifier would have been Lightsabers, which could be why they were banned following the takeover. I mean, you can’t have the local regimen shooting little Jimmy in the head because he had a glow-stick. But I digress.
I’m not sure if I’m getting the time line incorrect, but it seems the order to produce the clones came before or right around the time Anakin was introduced to Senator Palpatine (he would be a kid at this point). Did Palpatine foresee Anakin joining him on the Dark Side, or was there some other kind of exclusion involved?
I’ve searched the official sites and wikis, but nothing seems to address this.
“Programmed”? As in embedded in their DNA or something?
No. Order 66 was an order. Boss says do it, we do it. They were bred for discipline and following orders. The specific orders were to be determined later.
Per season 6 of The Clone Wars, the clones were indeed hardwired to have a homicidal dislike of Jedi, with a suppression of that instinct built in until such time as Order 66 was necessary.
Anakin was no longer a Jedi by the time of Order 66. Also note that 1) Darth Plagueis, Palpatine’s master, may have created Anakin (per dialogue in Revenge of the Sith) and 2) in the final scenes of The Phantom Menace, Palpatine hints that he already has his eye on Anakin.
Not so much a draft as an option that wasn’t implemented.
It’s actually basic military procedure - units receive lists of options to follow in responses for various eventuality. So if, say, you have in an attack in Sector C, the highest ranking officer will say, “Activate Option 11”, and everyone will open their options booklet and see what they each have to do. It saves time.