You don't say?
Huh. Well, that's a surprise to me. Though looking at the Mona Lisa illustration, I can see the resemblance.

: In the Feast of Bones article put up on b.net a few years back, they
: mentioned that the Juggernaut was what remained once the FSC began to take
: over, converting a combat form into something more, to the point where the
: original host's body no longer existed.

I've either forgotten about that, or never read it in the first place. Interesting.

: I kind of wonder if that might be part of what causes some of the drastic
: changes in the (theoretical, because it's just a simulation) Spartan
: combat forms.

I draw a clear line between canon and multiplayer fluff. RageSpartans and Holodecks don't make the cut.

: I think it's more likely to assume that some of the Librarian's samples were
: also stored on one of the Didact's shield worlds, but just like
: Installation 05, some of them broke out at one point.

Broke out at some point due to what interference? And from where? The inside was clean until the Spirit of Fire came through. Why would Flood samples be stored on the surface? If you stored them within the FDS, you have automatic quarantine and security: If something escapes, crank up the sun until you could melt steel on the interior surface.

: Although yes, I suppose
: the outbreak could be relatively recent, since we don't truly know when
: the Covenant accessed the shield world. Or do we? I actually didn't look
: through the Halo Wars timeline when I was piecing together this Flood
: theory.

It felt like a recent discovery, because it's five years into the war, and Regret is somehow convinced that they are absolutely necessary to finish the war quickly. Grabbing a human strikes me as a "We need to unlock this NOW" rather than a "We've been studying this for a few years, and we're pretty sure that this is the best way to unlock the warships."

And then there's the Covenant's later ignorance of the Flood. I can buy the idea of the Flood not being common knowledge if the Covenant's only contact was a handful of skirmishes twenty years before, but not if contact was prolonged to months or even years.

: Unfortunately it all depends on who's writing the story. That's why I think
: it's important to figure this stuff out, so future creators have a
: reference point when writing their stories.

Agreed.

: I suppose all of the above is possible. Not sure if there's any way to prove
: or disprove this though. :/

Good.
Some of the best theories of Halo's golden age were the ones that couldn't be proven or disproven.

: *Silentium spoilers*

: Considering that the Flood is what's left of the Precursors, and the
: Precursors created the Forerunner and humanity, I think they probably have
: a pretty good understanding of how our minds work. :)

Sheah, like Windows 8 programs are compatible with Windows 95?

Personally, I think that the Flood, the way it is created, the way its intelligence is organized, and the way it propagates, would give rise to a way of thinking alien to our own. Perhaps there's some genetically coded software that lets them communicate with us once they've attained the intelligence to run it. Maybe each individual Central Intelligence has to learn for itself.