Typical start:

- Set homeworld's prod slider to 100% planetside = 0% shipyard.  You don't build ships early anyways.

- Choose planet tiles to maximize tile and adjacency bonuses.  Homeworld probably concentrates on mp and rp.  Wealth I think you can defer to a colony planet later on.  (But Beta might monkey-wrench all that.)

- I think you always have a class-4 colonizable planet within range.  (For Terrans, it's Mars.)  Decide whether to colonize that with your starter colony ship, or wait for a bigger jackpot from early exploration.  It is debatable whether a Mars-class planet will replace its own colony ship fast enough to be worth the delay in building it up first.

- Turn-spree or click-hell.  Decide whether you want to optimize per-planet, per-turn to "exactly" finish 1 item with zero waste ... or just shrug it off and waste a few %.  Rule-of-thumb: if all of your queues, on average, finish 1 item every k turns, and you waste, on average, 0.5 turns of excess production per queue in each turn-of-completion, then your empire "wastes" 1/(2k) of its total production (so for k = 10, you waste 5%).  The AI on smart settings does not.  Hence, you can plan to just kick the AIs' collective butts by 6%+, and win anyways.  The click-hell approach trades off your play-time (and mouse clicks, to do binary search over and over again) for less waste.  (Later on, don't play multiplayer with the other kind of player, or you'll all go nuts.)

- For early ship exploration, try spiraling outward.  That way you're guaranteed to see all good stuff near you before you get lost far away.

- Survey every space junk, artifact, ship graveyard you can find.  The bad ones are only money.  The good ones are a free ship!

- Early ship builds are basically constructor and colonizer.  Customize both by deleting unneeded engines and life support -- no sense paying for a range of 29.9 hexes when its destination is only 5 hexes away.  You can make a double-constructor, i.e. with 2 constructor modules, which is cheaper than building 2 ships.  (Warning: in Alpha 0.31, you must actually own 2+ starbase improvement techs in order to double-upgrade, which does give you 2 modules -- you can save these as long as you want, and upgrade instantly as soon as you finish a juicy new tech.  If you move a double-ctor into a starbase when you have only 1 possible starbase improvement, it will simply dock there, and remain a separate ship -- boo.  Maybe that's changed.)

- Colony ships deduct 2.5 bp (billion pop) each, which is a hefty chunk of your source planet.  Hence I crank growth and food.  N.B. when you have multiple planets feeding 1 shipyard that completes a colonizer, you cannot control (at all?) from which planet it takes them.  Workaround: Manage the shipyard and remove N-1 of the planets for that turn only.  Then there's no ambiguity.

- Plan starbases carefully -- later on, they cost you proportional to the number you own (and you cannot scrap a starbase), i.e. the total cost is quadratic(!).  (Proof sketch: the sum of linear is triangular: SUM{i} (i) = n(n+1)/2 = O(n^2).)  On medium maps, your midgame ships can easily reach the far edge of the map.  On large maps, you'll eventually use forward starbases to let your scouts advance.

- Look for 2+ colonizable planets within "single starbase effect" (which incidentally got reduced from 6 hexes to 5 hexes).  One starbase with manuf / research bonuses will apply to all colonies in range.

Early tricks:

- Unanchor your shipyard, and drive it around.  It's got range-5 or range-6 sensors.  Even at 1 hex per turn, it can help you map a huge swath of nearby space before you bring it back.  You probably won't need to build a ship for the first 20 or so turns, while your homeworld is still building up its tiles anyways.  By the time you're ready to build ships, you should also know where to put your shipyard.  It can be anywhere within 6 hexes of your homeworld (+ your Mars if you took that path), so the difference between a good placement and a bad placement is up to 13 hexes, which is 3.5 extra turns of movement for a fast constructor / colonizer.

- (Very) rarely, you may have your Scout + Surveyor near enough to make a fleet before you survey an artifact.  Jackpot is a bonus to "all ships in fleet", e.g. +25% sensors or +25% movement.  (In my last Alpha 0.31 game, my surveyor got up to speed 12 and range-7 sensors before I colonized my 3rd planet!!  that was a very, very fun ship)

- Do not survey a wormhole   Your surveyor will be thrown halfway across the map, on average, and then it can only come straight home -- you'll lose control over it until then, and it might get shot down by Drengin's Lost Cutter)

My Alpha Terran start:

- Colonize Mars.  Build all mp with it: 2 factory, 1 farm.  Later, scavenge a factory to a Solar Power Plant.  When it finishes building, have it churn out ships.

- Research +% growth, then +food, then manuf/research.  You don't need to fight for a while, so weapons can wait.  (N.B. Beta planetary approval confounds this -- now you can trade off early production for massive growth bonus from high approval.  So maybe research food techs first, which incidentally got better because they lower your population pressure, which makes approval easier to maintain.)

- Build a starbase within range of Earth/Mars.  Add manuf/research improvements to it as fast as you research those techs.

Beta confounds:

- Approval bonus: For early game, this means you can trade off production for wealth/growth.  At the all-manuf or all-research extreme, your approval bottoms out to 70% or below, which is 0% or +10% bonus to growth/production/influence.  By setting enough wealth to offset your "population pressure", you can get to 100% approval, which is a massive +50% bonus.  Offhand, I think this is worthwhile even just for the growth alone.  But it needs more experiments.

- You can easily see the growth bonus from turn-to-turn.  Normal growth is +0.10 bc (billion pop) per turn, so +50% means +0.15, etc.

- I don't see the production bonus adding in anywhere.  I think it just quietly adds it to your next turn's production, but is not itemized in the tooltip list.  If you go from 100% approval to all-manuf, next turn you'll see your total mp drop significantly.  I think that's due to dropping from the +50% bonus tier down to the +10% or =0% bonus tier.

Clearly, more experiments are needed.  Preferably with Malevolence.

A1. Planet production

Each planet has base population (bp), in billions.  The wheel assigns pop to 3 axes:

• manuf (mp).  This is further splittable (by the slider bar) into your planetside build queue vs. your planet's shipyard build queue.  (Corollary: if you have no shipyard, or it's unanchored while you move it around, slide max left and build planet tiles.)
• research (rp).  This just pays toward your current Tech project.  I think you can switch tech projects at any time without losing any partial work -- just switch back to it later to finish it off.  (Useful, I guess, if you just started a 190-rp tech, but Drengin found you and you need a 57-rp detour for weapons fast)
• wealth (bc).  This stockpiles.  At any time, you can just buy a ship or tile queue item (which schedules it to complete that turn -- so only once per turn per queue).  These buys are at the exorbitant rate of 15 bc per 1 mp.  You'd be way better off just assigning 1 pp to produce 1 mp directly, than to assign 15 pp to produce 15 bc to buy 1 mp.  But it does mean that if you ever get like an 8:1 lead over an opponent, then you can devote 3/4 of your backfield to wealth production, colonize something on the frontier, and very quickly buy it full.

Corollary: You can use the $15 ratio to quickly compute how many turns a queue item really has remaining.  Select the item, hover over Buy It Now , and divide the price in bc by 15 to get mps.

With no bonuses at all, 1 population (pp) produces 1 of mp/rp/bc.  Your racial, planetary, tile (including adjacency), tech, and starbase bonuses add to this linearly.  Hover over any production column (mp, rp, or bc) to see all of its additive bonuses.  (Corollary: a Basic Factory's +10% mp, with no adjacency bonus because it's an island, could be a miniscule contribution to your overall manuf.  Later on, you may be getting +50% from two starbases in range, +30% from techs, +50% from Active Core (i.e. you dedicate such a planet to be a forgeworld), +20% from racial = +150%, for a total of 250% from non-tiles.  Compared to that, a +10% island is only a 1/25 increase in your total mps, or 4%.  If you replaced that Basic Factory with an Adaptive Farm for +4 food that increases the planet's max pop from 16 to 20, that's a +25% increase (eventually) in your max mp output.)

A2. Planetary Approval bonus (Beta!)

This is different.  I doodled with Excel, and I think I figured out how it works.  Your approval tier earns you a bonus to growth/production/influence.  Experiment to find the tier breakpoints.  "Population pressure" is a penalty that increases in magnitude the closer you get to your food limit.  Roughly:

• 100% approval = +50% bonus at 0% sum of penalties (wealth joy - population pressure)
• 95% approval = +40% bonus at -5%
• 85% approval = +25% bonus at -15%
• 70% approval = +10% bonus at -25%?
• less than that = 0% bonus (i.e. the Alpha 0.31 economy)

"+% growth" is self-explanatory.  Base growth is +0.10 bp per turn, per planet.  So your homeworld, which begins with 10.00 bp and has 12.00 food, would normally fill up after 2.0 bp growth, in 20 turns.  "+50% growth" means +0.15 bp, which would cut that to 13 turns.  Later, each colony ship you complete takes 2.5 bp from a planet, which takes 25 turns to grow back ... or less if you increase growth techs.  (So you can't just build an infinite stream of colony ships.)

"+% production" is not additive with the other +% bonuses.  Instead, it multiplies all 3 of your axes for next turn.  That's ... huge, I think.  So the +50% bonus for 100% approval means next turn you get 1.5x your pp in total production, which your wheel then distributes.  This approval bonus is already baked into the "raw research" and "raw wealth" figures you see in the hover lists (which contradicts the word "raw").

For example, if your homeworld with 10.00 bp, assigns 40% to wealth, and has +10% wealth, that should be 4.0 "raw wealth" +10% = 4.4 bc.  But if you had 50% bonus from last turn, it will display as 6.0 "raw wealth" = 6.6 bc.  Corollary: for the same population, it's better to be at 30% mp/rp with the +50% approval bonus than to be at 44% mp/rp with +0% bonus, because 30% of your people +50% behaves just like 45%.  (Don't worry if this section confuses you -- some of us have been here since GC2 + GC3a, and we're scratching our heads too.)

B1. Shipyard management.

• A planet can deliver mps to 0 or 1 shipyard (but not 2+).  Only the fraction of its mps set by the slider bar in the Govern window go to the shipyard.  (Corollary: In tile-build-up phase, set slider max left, to 100% planetside.  When no tiles remain to build or be improved, set slider max right.  In between those extremes, use whatever setting works for your current goals.)
• Every shipyard must be tied to 1+ planet (or you can't end turn).  It's ok to use a backwater planet 100+ hexes away just to hold its leash.
• A shipyard can receive mps from 1+ planets (as many as you like).  Caution: Finishing a colony or transport ship will take bp from one of the assigned planets.  Usually it's the one with most population, but I've seen that rule-of-thumb fail.  (Work-around: in the turn of completion, remove the N-1 other planets, and have the planet you want to draw down finish the ship on its own.)
• An unanchored shipyard, or one that was anchored this turn, ignores all incoming mps, and does not build anything.  You can move it 1 hex per turn while unanchored.  You can't end turn until you either move it or anchor it.  If you unanchor, move, and anchor in the same turn, it still doesn't build anything.  Any mps delivered to a shipyard that was unanchored this turn are simply lost, wasted.  (Work-around: during your homeworld tile-building phase, unanchor and drive your shipyard around for "free", since you're not building ships anyways.  Later, settle down and divert some mps to it.)

To assign planets to a shipyard, select (click) the shipyard, click Manage.  In the lower left corner, there's a list of all planets assigned to it. Click "Add" and "Remove".

• At range 6 hexes or less, each planet delivers 100% of its ship-building mps to its shipyard per turn.
• At ranges of 7+ hexes, penalties apply to each planet's production delivered to that shipyard (so I just never do that).
• In the silly case, you can have a monster planet generating a ton of production, throw away 99% of it, and deliver only 1 mp to a remote shipyard.  (Then you'd almost surely be better off setting the planet to generate bc, and just buy the ship outright.  That loses "only" 14/15 of your production.)

B2. Shipyard location

6 hexes is 1-2 turns of movement (until midgame ships).  It may be convenient to trundle your shipyard 6 hexes closer to a region of interest, and just build them thereat with zero penalty.  Early-game, this could be a cluster of planets to colonize.  Mid-game, it might be to move closer to (or further from) an enemy you're attacking.

Late-game, you could have a cluster of planets juggle an equal number of shipyards.  e.g. if you colonize Earth and Mars, you could park 2 shipyards at opposite corners of a 13-hex major hexagon, so they're both in range of both planets.  Then complete a build at 1 shipyard, instantly reassign both planets to the other shipyard, and it's like your next finished ship "teleports" that 13-hex gap for free.  You would need a 3rd planet to hold the leash of the fallow shipyard.  Bonus: while you're not using it, you can unanchor it and move it around.

C. Customizing ships

You can skip this until you're ready to plunge into it.  Designing new ship types is half the fun of this genre.  The simple half is to just fill the capacity with components.  The artistic half is to play Legos with your mouse until it looks better than the other guy's work of art.  (This does not interest me yet, so I just use the stock ship designs.)

For early builds, you can save mild cost and build time by shaving off components you don't need.  Colonizers and constructors have the curiously redeeming feature that they vanish when you use them, so you don't care how good or bad the rest of their components were, or if the ship was half-empty.  Count hexes to see what minimal range you need to colonize a planet or establish a starbase, then build a custom version of the ship that gets exactly that far.  Remove enough mass from the stock constructor, and you can fit a 2nd constructor module on it, which lets you make 2 upgrades with 1 ship.

Thanks a lot for the massive answer, so awesome!

Beta "rebalanced" shipyard sensor range from 6 hexes to 4 hexes

Upgrade is what you use to bring older ships to the state-of-the-art. If, say, you research improved engines, then those apply to all new ships, but having them on older ships requires you to Upgrade them. The same goes for any other upgrades.

Concerning the shipbuilder and ship capabilities, go to the Equip tab. There, you can outfit them with weapons, defenses, engines and anything else you could want.

Ships appear to upgrade wherever they are in space, they don't need to go to a planet or a shipyard.