Ok so how do shapeshifters work then? The way Stackpole wrote or the way the rules say?
According to the rules in Fourth Edition, and depending on whether it is a PC shapeshifter or an NPC shapeshifter.
It's been mentioned before, but Stackpole's novels were written when they were still creating Shadowrun. He had the ultimate artistic license, and yet he was trumped early into the game on a number of things ranging from shapeshifters to professional baseball in the canon.
Where are the rules about spirits of light?
Unwritten. GM Discretion, one supposes. It's with the rules for making a sandwich.
There has been a long policy among line developers to keep things vague or outright unknown, and that includes rules. However, just because there are no rules for something doesn't mean it can't happen/exist in Shadowrun.
Where are the rules about having all your cyber purged out and restoring your ability to use magic again?
Unwritten. GM Discretion, again. However, you can't say that regaining magic is not canon. Dr. Miles Swineburn had burned out his magic with too many Euro Wars implants. In
Portfolio of a Dragon, he gets his magic back after receiving the tarot deck Dunk left him.
In
Year of the Comet SURGEing and getting the Astral Sight effect gave your character Magic 1. Period. Essence be damned. That was funny as Hell to see on a character with a quarter point of Essence left. As I recall, that is what happened to the character in question. They had cybereyes, SURGEd, and voila! New eyes. That isn't a rules thing. It's a RP thing written by the guy who wrote most of the SR2 magic rules. In fact, this is what the Astral Sight effect does:
Astral Sight (6)
The character undergoes a limited Awakening, acquiring a Magic rating of 1. This Awakening allows her to open her perceptions to the astral plane and assense, just like a magician (see Astral Perception, p. 171, SR3). She can also now learn the Magical skills of Aura Reading and Enchanting. She cannot astrally project, however, nor does she gain access to any other magical abilities or skills.
This effect cannot be applied to Awakened characters (including adepts).
So either Kenson said to Hell with the rules, that there is more to the effect that what is in YotC, it was an unpublished SURGE effect, or it was something completely different. Doesn't matter. However, I can tell you that Magic in the Shadows says that only Awakened characters can initiate and there is an interpretation that says the list in parentheses that lists full magicians, aspected magicians, and adepts is not, and could not be comprehensive. Since technically the character is Awakened (limited Awakening is still Awakening) there is an argument that I've seen successfully made that a character with astral sight can Initiate and if they are willing to eat the karma costs for buying the magician or adept Edge in-game, could become "more."
There's no rule that says you can, but there's nothing that says you can't. And while I have recently made
my thoughts on authorial intent and interpretation known if the guy who wrote the magic rules says it's possible and in canon it happened, that is a strong argument to make to a GM.
There were references to the physical events of the finale in Beyond the Pale with the locus in at least one sourcebook, however. Tommy Talon's adventure to whatever metaplane he was in when he crossed Ghostwalker's path is canon as of Street Legends.
As for Bogotá, there's no map, but as I recall the comment in regards to that mini-sub is not ... comprehensive. But just as a reminder this is also the game where an entire country (Luxembourg) is now part of a tri-national irradiated zone, Libya is a post-nuclear wasteland that exists solely for corporate war games, most of the Los Angeles basin (along with other chunks of California and Baja California) is underwater, an localized EMP bomb somehow crippled the Panama Canal so that Aztechnology had to go and carve a new one through Nicaragua in less than five years, and an island emerged in the middle of the Pacific Ocean one day filled with natural orichalcum.
Shadowrun is not reality. However, Patrick may be too modest to say it but the fact is that Shadowrun isn't Dr. Who. There is a canon. That canon, like all canons going back to Church canon law, which is where we get the name, is defined by arbiters: Us, the freelancers and artists (Oh, yeah. The art has been, AFAIK, canon.) as permitted by the line developers. That's why I don't mind that Lofwyr has stats. Anyone can kill him in their game, but he's not dead in the canon continuity unless we say he is.
We are like a buffet. We put out what we think will be most enjoyable and useful for your consumption, and then let you have at it. Bring in your own food if you like. However, the selection is what the selection is. Unless I'm told differently, the events of the Dragon Heart Saga are canon. You don't have to like it or use it, but that's the way it is as the game is being continually constructed even if it never comes up again.