Note: I've tried my best to guess which items are varaibles, which are functions, and which libraries they belong to. Please fix any errors or update the list with new information.
Note: three question marks ("???") mean I don't know, or am unsure about the accuracy of my guess.
Legend
<Namespace> <Library File> (<Usage Context>)
Functions
<Function>
"<Error Message>"
<Function>
<Function>
...
Variables
<Variable>
<Variable>
<Variable>
...
List
??? "EngineBurn.cpp"
??? "EngineGlow.cpp"
Functions
setEngineGlow
"Invalid type for first arguement"
"Invalid type for eighth arguement - glowColour"
"Invalid type for seventh arguement - maxBlur"
"Invalid type for sixth arguement - blurFullOnDistance"
"Invalid type for fifth arguement - blurStartDistance"
"Invalid type for fourth arguement - flickerFrequency"
"Invalid type for fourth arguement - flickerMax"
"Invalid type for third arguement - flickerMin"
"Invalid type for second arguement - maxTranslation"
??? "EngineTrailSystem.cpp"
Functions
setEngineTrail
"Invalid type for second arguement - diameterFactor"
"Invalid type for second arguement - ufactor"
"Invalid type for second arguement - uscrollFactor"
"Invalid type for second arguement - bulgeFrequency"
"Invalid type for second arguement - textureName"
"Invalid type for second arguement - lingerTime"
"Invalid type for second arguement - index"
"Invalid type for first arguement"
??? "gameSettings.cpp"
luaappmainui ??? (Autoexec, UI)
Possibly the same functions as luagamemainui.
luaappmisc ??? (Autoexec, UI)
luagamesettings ??? (Autoexec, Gamerule)
luagamemainui ??? (Autoexec)
??? ???
statlogging ??? (Autoexec, UI, Gamerule, AI)
??? ???
??? ???
??? ??? (AI)
??? ???
??? ???
??? ??? (AI)
luacpu ??? (Gamerule)
luanis ??? (Gamerule)
luanisdebug ???
??? ???
These look like variables.
SMPTEOff
SMPTEOn
stayFadedAtEnd
runScar
setResourceValue
setPlayer
destroyEffect
triggerEffect
setEnginePower
startEffectEvent
ambientSoundVolume
engineSoundVolume
navlightPower
navlightSpeed
setInHyperspace
hyperspaceOut
hyperspaceIn
trailMove
trailZero
hideUniverse
pauseUniverse
focus
focusAtEnd
newNIS
setMADState
meshAnimPause
meshAnimStop
meshAnimStart
keepMovingAtEnd
remainAtEnd
lockLOD
health
fleetSpeechEvent
speechEvent
soundEvent
SFXVolume
speechSetDir
fire
haltAttack
attack
death
musicStartAtEnd
musicStop
musicStartFade
musicStart
cameraLeave
cameraFadeIn
cameraBlendIn
cameraCut
vincible
invincible
show
hide
displayCard
fadeSet
fadeTo
nisOut
wideScreenOut
wideScreenIn
??? ???
These look like variables.
listObjectiveItem
listEvents
LuaMenuSupport "MenuSupport.cpp" (Autoexec, UI, Gamerule)
luagameio ??? "MenuSupport.cpp" (UI, Autoexec)
luagamemisc ??? (UI, Autoexec)
lualoadlevel "LuaLoadLevel.cpp" (Level)
luarender ??? (Autoexec)
luashipdebug ???
??? MadState "MADState.cpp"
??? "WinMain.cpp"
??? Mission level ???
luauserinterface ??? (Autoexec, UI, Gamerule)
??? LuaRuleSystem ??? (Autoexec, UI, Gamerule)
??? ScarEventSystem ??? (Gamerule)
luacamera "LuaCamera.cpp" (Autoexec, Gamerule)
luauniverse "LuaUniverse.cpp" (Gamerule, Autoexec)
luaplayer "LuaPlayer.cpp" (Gamerule)
??? Scar "Scar.cpp"
luafx "LuaFX.cpp" (Gamerule)
luashadow "LuaShadow.cpp" (Gamerule)
luasound "LuaSound.cpp" (Gamerule, Level)
luafog "LuaFog.cpp" (Level)
lualight "LuaLight.cpp" (Gamerule, Level)
??? ??? (Autoexec, UI)
luaATI "LuaATI.cpp" (Gamerule)
luahyperspace "LuaHyperspace.cpp" (Gamerule)
luaping "LuaPing.cpp" (Gamerule)
luasensor "LuaSensor.cpp" (Gamerule)
luateamactions "LuaSobGroupActions.cpp" (Gamerule)
luateamquery "LuaSobGroupQuery.cpp" (Gamerule)
luaobjectives "LuaObjectives.cpp" (Gamerule)
luasubtitle "LuaSubtitle.cpp" (Gamerule)
luacampaign "LuaCampaign.cpp" (Gamerule)
List of Library Files
"AnimEventContainer.cpp"
"AppInit.cpp"
"AsctObjectLoad.cpp"
"ATI.cpp"
"AttackCommand.cpp"
"AttackStyle.cpp"
"BattleScarManager.cpp"
"BattleScarPoint.cpp"
"BattleScarTrail.cpp"
"BTG.cpp"
"BuildData.cpp"
"BuildManager.cpp"
"campaign.cpp"
"Collision.cpp"
"DecalRefMeshRegistry.cpp"
"DirectConnectionScreen.cpp"
"DockCommand.cpp"
"DockQueue.cpp"
"DogFightAttackStyle.cpp"
"DustCloud.cpp"
"EngineBurn.cpp"
"EngineGlow.cpp"
"EngineTrailSystem.cpp"
"FamilyList.cpp"
"FinalBuildMenu.cpp"
"FlightManeuverManager.cpp"
"Formation.cpp"
"FormationLaunchCommand.cpp"
"FormationPatternManager.cpp"
"FXManager.cpp"
"FXMemory.cpp"
"GameMenu.cpp"
"GameOptions.cpp"
"GameRulesLibrary.cpp"
"gameSettings.cpp"
"Graphic.cpp"
"HardPointStatic.cpp"
"HW2CpuPlayer.cpp"
"Hw2Identify.cpp"
"HyperSpaceCommand.cpp"
"HyperspaceManager.cpp"
"ITweak.cpp"
"LaunchCommand.cpp"
"LevelManager.cpp"
"LobbyScreen.cpp"
"LuaATI.cpp"
"LuaCamera.cpp"
"LuaCampaign.cpp"
"LuaLoadLevel.cpp"
"LuaPing.cpp"
"LuaPlayer.cpp"
"LuaSobGroupActions.cpp"
"LuaSobGroupQuery.cpp"
"LuaSound.cpp"
"LuaUniverse.cpp"
"MADState.cpp"
"MainUIRender.cpp"
"MenuSupport.cpp"
"Missile.cpp"
"ModifierEffect.cpp"
"ModifierMultiplier.cpp"
"movie.cpp"
"NewProfile.cpp"
"NewUIScreen.cpp"
"NISMotion.cpp"
"ParadeCommand.cpp"
"ParadeManager.cpp"
"ParadeStaticData.cpp"
"PersistantData.cpp"
"Ping.cpp"
"PlayerProfile.cpp"
"QueueListBoxItem.cpp"
"Race.cpp"
"RallyParadeCommand.cpp"
"ReactiveFleet.cpp"
"recorder.cpp"
"region.cpp"
"RenderModelScars.cpp"
"ResearchData.cpp"
"ResearchManager.cpp"
"SaveGameData.cpp"
"savestream.cpp"
"Scar.cpp"
"scripting.cpp"
"sctBasicGlobals.cpp"
"sctMatVec.cpp"
"SensorPingManager.cpp"
"ship.cpp"
"shipHold.cpp"
"SobFactory.cpp"
"sobstatic.cpp"
"SoundEntity.cpp"
"SoundEventHandler.cpp"
"SoundManInit.cpp"
"SoundParamManager.cpp"
"SPMissionSelect.cpp"
"Squadron.cpp"
"StrikeGroup.cpp"
"StrikeGroupFormationManager.cpp"
"StyleSheet.cpp"
"SubSystemType.cpp"
"TacticalIcon.cpp"
"TacticalOverlay.cpp"
"Tactics.cpp"
"TeamColour.cpp"
"UIGraphic.cpp"
"UnitCaps.cpp"
"Universe.cpp"
"Volume.cpp"
"WeaponFire.cpp"
"WeaponStatic.cpp"
"WinMain.cpp"
List of Namespaces
??? LuaRuleSystem ??? (Autoexec, UI, Gamerule)
??? MadState "MADState.cpp"
??? Mission level ???
??? Scar "Scar.cpp"
??? ScarEventSystem ??? (Gamerule)
debugrender ??? (Autoexec, UI)
luaappmainui ??? (Autoexec, UI)
luaappmisc ??? (Autoexec, UI)
luaATI "LuaATI.cpp" (Gamerule)
luacamera "LuaCamera.cpp" (Autoexec, Gamerule)
luacampaign "LuaCampaign.cpp" (Gamerule)
luacpu ??? (Gamerule)
luafog "LuaFog.cpp" (Level)
luafx "LuaFX.cpp" (Gamerule)
luagameio ??? "MenuSupport.cpp" (UI, Autoexec)
luagamemainui ??? (Autoexec)
luagamemisc ??? (UI, Autoexec)
luagamesettings ??? (Autoexec, Gamerule)
luahyperspace "LuaHyperspace.cpp" (Gamerule)
lualight "LuaLight.cpp" (Gamerule, Level)
lualoadlevel "LuaLoadLevel.cpp" (Level)
LuaMenuSupport "MenuSupport.cpp" (Autoexec, UI, Gamerule)
luanis ??? (Gamerule)
luanisdebug ???
luaobjectives "LuaObjectives.cpp" (Gamerule)
luaping "LuaPing.cpp" (Gamerule)
luaplayer "LuaPlayer.cpp" (Gamerule)
luaplayer_console ??? (Autoexec)
luarender ??? (Autoexec)
luasensor "LuaSensor.cpp" (Gamerule)
luashadow "LuaShadow.cpp" (Gamerule)
luashipdebug ???
luasound "LuaSound.cpp" (Gamerule, Level)
luasubtitle "LuaSubtitle.cpp" (Gamerule)
luateamactions "LuaSobGroupActions.cpp" (Gamerule)
luateamquery "LuaSobGroupQuery.cpp" (Gamerule)
luauniverse "LuaUniverse.cpp" (Gamerule, Autoexec)
luauserinterface ??? (Autoexec, UI, Gamerule)
statlogging ??? (Autoexec, UI, Gamerule, AI)