Here is a list of all documented files with brief descriptions:

FGAccelerations.cpp
FGAccelerations.h
FGAccelerometer.cpp
FGAccelerometer.h
FGActuator.cpp
FGActuator.h
FGAerodynamics.cpp
FGAerodynamics.h
FGAircraft.cpp
FGAircraft.h
FGAngles.cpp
FGAngles.h
FGAtmosphere.cpp
FGAtmosphere.h
FGAuxiliary.cpp
FGAuxiliary.h
FGBuoyantForces.cpp
FGBuoyantForces.h
FGColumnVector3.cpp
FGColumnVector3.h
FGCondition.cpp
FGCondition.h
FGDeadBand.cpp
FGDeadBand.h
FGDistributor.cpp
FGDistributor.h
FGElectric.cpp
FGElectric.h
FGEngine.cpp
FGEngine.h
FGExternalForce.cpp
FGExternalForce.h
FGExternalReactions.cpp
FGExternalReactions.h
FGFCS.cpp
FGFCS.h
FGFCSChannel.h
FGFCSComponent.cpp
FGFCSComponent.h
FGFCSFunction.cpp
FGFCSFunction.h
FGFDMExec.cpp
FGFDMExec.h
FGfdmSocket.cpp
FGfdmSocket.h
FGFilter.cpp
FGFilter.h
FGForce.cpp
FGForce.h
FGFunction.cpp
FGFunction.h
FGGain.cpp
FGGain.h
FGGasCell.cpp
FGGasCell.h
FGGroundCallback.cpp
FGGroundCallback.h
FGGroundReactions.cpp
FGGroundReactions.h
FGGyro.cpp
FGGyro.h
FGInertial.cpp
FGInertial.h
FGInitialCondition.cpp
FGInitialCondition.h
FGInput.cpp
FGInput.h
FGInputSocket.cpp
FGInputSocket.h
FGInputType.cpp
FGInputType.h
FGJSBBase.cpp
FGJSBBase.h
FGKinemat.cpp
FGKinemat.h
FGLGear.cpp
FGLGear.h
FGLinearization.cpp
FGLinearization.h
FGLocation.cpp
FGLocation.h
FGMagnetometer.cpp
FGMagnetometer.h
FGMars.cpp
FGMars.h
FGMassBalance.cpp
FGMassBalance.h
FGMatrix33.cpp
FGMatrix33.h
FGModel.cpp
FGModel.h
FGModelFunctions.cpp
FGModelFunctions.h
FGModelLoader.cpp
FGModelLoader.h
FGMSIS.cpp
FGMSIS.h
FGMSISData.cpp
FGNelderMead.cpp
FGNelderMead.h
FGNozzle.cpp
FGNozzle.h
FGOutput.cpp
FGOutput.h
FGOutputFG.cpp
FGOutputFG.h
FGOutputFile.cpp
FGOutputFile.h
FGOutputSocket.cpp
FGOutputSocket.h
FGOutputTextFile.cpp
FGOutputTextFile.h
FGOutputType.cpp
FGOutputType.h
FGParameter.h
FGPID.cpp
FGPID.h
FGPiston.cpp
FGPiston.h
FGPropagate.cpp
FGPropagate.h
FGPropeller.cpp
FGPropeller.h
FGPropertyManager.cpp
FGPropertyManager.h
FGPropertyReader.cpp
FGPropertyReader.h
FGPropertyValue.cpp
FGPropertyValue.h
FGPropulsion.cpp
FGPropulsion.h
FGQuaternion.cpp
FGQuaternion.h
FGRealValue.cpp
FGRealValue.h
FGRocket.cpp
FGRocket.h
FGRotor.cpp
FGRotor.h
FGRungeKutta.cpp
FGRungeKutta.h
FGScript.cpp
FGScript.h
FGSensor.cpp
FGSensor.h
FGSensorOrientation.h
FGSimplexTrim.cpp
FGSimplexTrim.h
FGStandardAtmosphere.cpp
FGStandardAtmosphere.h
FGStateSpace.cpp
FGStateSpace.h
FGSummer.cpp
FGSummer.h
FGSurface.cpp
FGSurface.h
FGSwitch.cpp
FGSwitch.h
FGTable.cpp
FGTable.h
FGTank.cpp
FGTank.h
FGThruster.cpp
FGThruster.h
FGTransmission.cpp
FGTransmission.h
FGTrim.cpp
FGTrim.h
FGTrimAnalysis.cpp
FGTrimAnalysis.h
FGTrimAnalysisControl.cpp
FGTrimAnalysisControl.h
FGTrimAxis.cpp
FGTrimAxis.h
FGTrimmer.cpp
FGTrimmer.h
FGTurbine.cpp
FGTurbine.h
FGTurboProp.cpp
FGTurboProp.h
FGUDPInputSocket.cpp
FGUDPInputSocket.h
FGUDPOutputSocket.cpp
FGUDPOutputSocket.h
FGWaypoint.cpp
FGWaypoint.h
FGWinds.cpp
FGWinds.h
FGXMLElement.cpp
FGXMLElement.h
FGXMLFileRead.h
FGXMLParse.cpp
FGXMLParse.h
JSBSim.cpp
JSBSim.minimal.cpp
LagrangeMultiplier.h
string_utilities.h