Hello again everyone,
I've built up quite a bit of ruling questions lately and would like some calcification on them.

1) How do you determine who does what actions first when using things that happen after initiative like intuition or Surprise Move? Is it whoever won initiative gets to pick who does what actions first? Or is it whoever lost initiative uses intuition or Surprise Move first and then whoever won uses theirs?

1a. Whoever goes first did all of their pre round stuff and then the other player.
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2) Does Mutant cyborg experimentation allow for a rapport ability that decreases the cost of droids to also decrease the cost of allies I am bringing in that Mutant cyborg experimentation applies to that were not originally droids?

2a. Need to check on that one, but I think probably not.
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3) Does Penetration go through things like Dark armor, battle armor, etc? Or is it only to the damage reduction ability specifically?

3a. Just DR.
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4) Does Commando Droid Officer's commander effect's damage bonuses stack? Like one part of it says Commando Droids get +10 damage. And then another part of it's commander effects allows for a Commando Droid to make an immediate attack at +10 damage. Would both of these effects stack to allow for that commando droid to have a +20 bonus to damage on it's one immediate attack? I was told that same stat bonuses do not stack if they are from commander effects but this seemed odd then to have both bonuses on the same commander effect if they could not stack?

4a. Straight bonuses from CEs don't stack so no based on the question. I didn't double check the CE.
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5) Does Don't Tell Me the Odds affect the Force power Anticipation?

5a. Only special abilities.
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6) Can Sith Holocron's ability Dark Allure affect a cloaked character? It does not say target, it just says a character within 6 squares. Does this mean it can also work through walls as long as that character is within 6 squares of it?

6a. It is just within 6 and doesn't target, so yes.
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7) Does using Jedi Mind Trick not count as an action that a character is making and can just be used at the end of the character's turn? For example one of my friends used Obi-Wan (who has Greater Mobile Attack) and moved 5 squares and made his attacks and then moved up 1 more square and on that square used Jed Mind Trick 3. Is this legal? To me I thought Jedi Mind Trick was a sort of replaces attacks kind of thing and not something like Sith Rage that can be used whenever. Does this mean that Jedi Mind Trick can be used twice in a row with Master of the Force 2?

7a. Your friend is right. We usually call these abilities zero time abilities because they don't replace anything. They are used "on" your turn though, not "at the end" of the turn. So if you use a replaces-turn ability you cannot also use a zero time ability.
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8) When using Force Essence, does the newly Force Ghost character come in activated or unactivated? Or is it dependent on what the current state of the character that has Force Essence was before Force Essence was triggered?

8a. I didn't check the glossary but characters that replace others generally come in unactivated.
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9) Can Bacta Tank learn Heal 10? A friend recently used Medical Supplies on a Bacta Tank and I thought that was too silly to actually work. Is this allowed?

9a. Silly but legal. I made a Bacta Tank of Doom squad to make one as powerful as possible.
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10) How do you determine if an AT-AT applies for Opportunist or Cunning? If only 1 of its actions is covered up and it still has more to go then does it count as unactivated or activated for the purpose of these types of abilities?

10a. No idea. Good question.
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11) If someone uses something that makes a character become activated but they used it on an AT-AT, can they choose which action gets activated like one of their blaster activations instead of their move ones? Or is it the opponent that gets to pick which option is being activated.

11a. No idea. Good question.
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12) If a character rolls a 1 against Betrayal or fails the save for Turn to the Dark Side, do they get a chance to reroll that with a Force point or once they failed it the first time, it is too late for them to reroll because they now belong to your opponent and you no longer have a say in their ability to reroll?

12a. They can reroll.
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