This table shows all actions involving planets. The left column shows the PControl stages, in chronological order. The middle column contains all actions affecting happiness or population (like "taxation happens before growth"), the right-most column contains all actions affecting minerals and buildings (like "beam-up-multiple happens before lfm" (hint, hint)). The "Details" column contains a link to the relevant section of this document, if there is one.

StageHappiness/PopulationMinerals/IndustryDetails
Turn Processing (Phase 1)Colonists transferred to/from own shipsResources transferred to/from own ships. Resources spent for planetary buildings, starbases, starship parts, ammunition (starbases are built at this time, everything else already appeared at clientside).
LargeMeteors, MeteorShowersMeteors might bring down happiness and kill people.Meteors and meteor showers add minerals to planet core.Formulas
DeluxeSuperSpyIonic pulse triggered by Super Spy Deluxe may kill defenses
CargoDumpGround combatFormulas
TrainingShips gather supplies for training
GatherMissionShips gather stuff
SpecialMissions_1Lizards HissFormulas
BuildFighters, BuildTorpedoesShips gather stuff
ShipBuilding_1Cloning might consume minerals.
DumpOldBasePartsStarbases recycle old starship parts
BaseMissions_1Starbases first recycle ships, then maximize defense or load torps onto ships
FreeFightersStarbases build "free" fighters
GloryDevicesGlory devices kill people and toast Amorphous nativesGlory devices damage planetFormulas
ColonizeMissionColonize ships bring clansColonize ships bring mineralsFormulas
BaseMissions_2Starbases refuel ships or unload them
CombatPopulation might be killed in combat.
Happiness change if planet is captured.
Defense might be destroyedEffects on planet, Combat
TerraformingTerraforming makes environment more pleasant for inhabitants.
SensorSweepSensor Sweep might discover planets according to their industryFormulas
SpecialMissions_2Pillage / RGA might make people unhappyPillage / RGA will destroy stuff, Dark Sense reports amounts afterwardsFormulas
PlanetaryProductionMining, supply production, then trans-uranium decayFormulas
PlanetaryHappinessif planet is unowned or happiness is 29 or lower, taxes are set to 0. Then, happiness changesFormulas
PlanetaryTaxationTax collectionFormulas
PlanetaryGrowthGrowthFormulas
PlanetaryLossesClimate deaths, then losses through riotsOverpopulation eat supplies, then structure decay, then losses through riots, then Amorphs eating colonistsFormulas
ShipBuilding_2Cloning might consume minerals.
AssimilationCyborgs assimilate nativesFormulas