Doh! Someone who actually reads the manual... Sorry, like Yarlen said we had to refine some stuff after it went to print and there is also so much stuff to cover that we'd need triple the pages. Hopefully, for the most part the manual + tutorails + tooltips/infocards will cover most players. We'll definately try and improve the infocards in the next build based on feedback like this.
So I have a mess of questions based on a recent build -- which includes the manual, so don't give me any of that RTFM guff! -- and I figured maybe some of you beta testers or even someone from Ironclad could help a fella out.
1) I'm a bit confused about how Trade Ports and Refineries work. Do they simply spawn cargo and refinery ships, which flit about earning me money and resources? Or does it matter where and how many I build? For instance, if I've got a juicy ice planet with four crystal mines, will building a refinery here help my crystal income more than if I'd build it at, say, an asteroid providing metal? Similarly, the manual implies I need at least two Trading Ports to make money. Should I be building these at a maximum distance from each other, in pairs? Does distance from capital matter? Because based on the manual and the otherwise excellent tooltips, I can't tell how I'm supposed to be using these buildings.
The trade/refinery ships autospawn though the number depends on the race, research, and Advent don't get refinery ships (they have a different mechanic). W/r to tradeports, the distance and connectivity matters. You can hover over the credits tab at the top to see a white line showing your longest direct path (which is different than "longest path ala Settlers of Catan") and how much each planet is bringing in via trade. Nodes that can't be colonized don't count against your path. Its very beneficial to trade with other players because it makes it much easier to get a long and unconnected trade route. You can trade with enemies, your tradeships won't give you vision of their territory and vice versa. Refineries work differently. They have a limited range and will give you bonus metal/crystal based on whatever is within reach of the refinery (I believe its 1 jump in your build). The Advent's refineries/tradeports are actually the same building but can switch modes and their refinery only works in the existing gravity well. Finally, and most importantly, destroying enemy tradeships gives you good $$ and destroying their resource ships gives you good resources. Naturally, it harms the enemy income rates as well. I've survived in huge multiplayer games just by pirating tradeshisp to fund the rebuilding of my glorious empire 
2) Having only played two of the races, I see a lot of undocumented stuff in the tech trees. What are long range jumps? Because upon researching this tech, I didn't see any difference in how my ships travelled. And worm hole stabilization sounds good and well, but I didn't see any worm hole traveling as near as I could tell. Also, one of the advanced techs reduces the mass of my ships. Okay, great. I'm all for mass reduction! But, uh, what does it do in the game?
Long jumps is the ability to jump to stars. Only applicable when there are other stars. Wormhole technology is for when the map has wormholes. Ignore them both if neither exists in your map. Mass Reduction reduces the mass of your ships allowing them to accelerate and turn faster.
3) So one planet has a crown-looking icon. That's my capital. So far, so good. Another planet has a sort of caret underneath it. Except in the empire tree, the caret is at the 45 degree position. What's that supposed to mean?
This indicates the presence of an artifact. If you read the infocard (tooltip) it should say that either you have one there, or you detect that an enemy has uncovered something powerful (i.e. the planet is glowing with awesomeness, you should go take it away from whoever is hording all the goodness for themselves)
4) I see a lot of possibility in setting my fleets on Hold Position and then carefully using individual elements, such as carriers and missile ships. Is there any way to set facing for formations, because it would help for those of us who want to try some tactical min/maxxing?
It's been requested and is planned for a future content update. It is fairly easy to tell them to move slightly in the direct you want and the leader will just rotate in place causing the rest of the formation to wheel. You can tab (and shift tab) through the selection to get the guy you are interested in using as the focal point. Tab and shift tab behavior is remarkably improved in the nit pick polish build we are working on now.
5) I love hotkeys! Love 'em! I can't get enough of 'em! So, is there a hotkey to collapse or expand all the pins on the empire tree? I want one.
Damn I thought we hotkeyed everything anyone would need (take a look at the massive list in the hotkey options page) but we didn't get that one. We will add it in the next content update. Just incase you didn't know though -> tilde pins/unpins, and ctrl-tilde unpins everything. For sake of ease, most of the hotkeys line up spatially on the keyboard with where they would be positioned on the action grid (e.g. (0,0) is q, (0,1) is W etc) so you just have to memorize the position instead of pneumonics and its triply easy because things of similiar function always hold the same position (even across factions).
6) Planets with a porous core have a gravity well radius of -33%. Not that I can tell. Is this working, or am I misunderstanding what the red 33% means?
It's probably difficult to tell without a frame of reference. I checked and it is working correctly, your ships will reach the edge sooner and arrive closer (well depending on where you jumped from ofcourse). Actually I should bring this advanced topic up which unfortunately also isn't documented. The position you jump from determines where in the next gravity well you arrive (if you've already explored the destination). Leave from the left, arrive on the left, leave from the near edge, arrive on the near edge etc. It's a design decison to solve an early beta problem where people would leave monster defense forces right at the center of the phase lane where they knew enemies would arrive.
Okay, that's it for now. I'm sure I'll have more questions, because I'm playing the daylights out of this thing. Awesome work, Ironclad!
-Tom
We will answer anything you got. Since the game's been in beta for so long I'm sure whatever you have has come up already and there is either a way to do it or a good reason why it hasn't been done 