The references you should need the most are :
Bot TutorialSysvarsOperatorsEpigenetic memmoryAlso you should start out with the F3 league (In the Bot tavern), it also contains a lot of tutorial bots to practice on (Each of them is a copy of the previous one with one added gene, making it easy to se the effect and value of that gene).
As for the questions :
What is the difference between native and non-native species?
No idea... don't even know what you're talking about... is it subspecies ? From evo sims ?
What is voluntary movement?
Using .up .dn .dx or .sx will make your bot move in that direction, that's volontary movement. (Involontary movement would be getting moved by other means)
Why is sexual reproduction used?
You don't have to use it, it's just an option for evo sims... and currently the most powerfull weapon in all the leagues where it's legal (But I don't think that was the intention).
I've read that you no longer need cond line.
You need it if you wan't conditions for an entire gene to get triggered, but other than that you can write conditions inside the gene (Just remember they don't get and'ed). Any line in a gene will check the boolean stack to see if it should be executed.
Why would older bot's act stupid in the newer versions?
Too many reason to explain it all, physics changes, eye changes asf asf...
Why is Wiki out of date (someone said it) when it's the first thing that pops up on Google when someone searches for DarwinBots?
Anyone can update the Wiki... if you think something is out of date or missing just link to the page in the forum or fill it out if you know the answer...
What is focal eye?
.focuseye sets the eye that you use to focus with, meaning the eye you can extract refvars from... (Like *.refeye and such)