2) Enhanced Ability is Continuous, therefore taking it down to Permanent is a -1 flaw, I believe. (If Enhanced Ability was Sustained, it'd be a -0/ flaw.)
3) The intent of the multiple minions is that they'll all be represented in the tactical console. If just one minion was added, you'd lose that.
Thanks for the other bug reports - I'll put them on the list.
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