Here is a list of all files with brief descriptions:

AddedMass.cpp
AddedMass.h
ADR.cpp
ADR.h
Allocation.h
analyticalSolutions.c
analyticalSolutions.h
ArgumentsDict.cpp
ArgumentsDict.h
ArrayRef.h
BoundaryConditions.cpp
mprans/BoundaryConditions.cpp
canalyticalSolutions.c
cElastoPlastic.cpp
cfemIntegrals.c
ChBodyAddedMass.cpp
ChBodyAddedMass.h
ChVariablesBodyAddedMass.cpp
ChVariablesBodyAddedMass.h
clapack.c
CLSVOF.cpp
CLSVOF.h
cMeshAdaptPUMI.cpp
cmeshTools.cpp
cMoveMeshMonitor.cpp
cnumericalFlux.c
CompKernel.h
CouplingFSI.cpp
cpartitioning.cpp
cpostprocessing.c
cpskRelations.cpp
createAnalyticGeometry.cpp
createAnalyticGeometry.h
cRichards.cpp
cshockCapturing.c
csmoothers.c
csparsity.cpp
csubgridError.c
cSubsurfaceTransportCoefficients.cpp
ctimeIntegration.c
ctransportCoefficients.c
cTwophaseDarcyCoefficients.cpp
densityRelations.h
Dissipation.cpp
Dissipation.h
Dissipation2D.cpp
Dissipation2D.h
Domain.cpp
Domain.h
Dpythag.cpp
druckerPrager.h
Dsvbksb.cpp
Dsvdcmp.cpp
DumpMesh.cpp
DumpMesh.h
ElastoPlastic.h
equivalent_polynomials.cpp
equivalent_polynomials.h
equivalent_polynomials_coefficients.h
equivalent_polynomials_coefficients_quad.h
equivalent_polynomials_utils.h
ErrorResidualMethod.cpp
femIntegrals.c
femIntegrals.h	A library of functions for computing the discrete finite element formulations
Fenton.cpp
flcbdfWrappers.cpp
flopTest.c
Fourier.cpp
GN_SW2DCV.cpp
GN_SW2DCV.h
Headers.h
Inout.cpp
Isosurface.c
jf.h
Kappa.cpp
Kappa.h
Kappa2D.cpp
Kappa2D.h
mcdp.h
MCorr.cpp
MCorr.h
MCorr3P.cpp
MCorr3P.h
mesh.cpp
mesh.h
MeshAdapt.cpp
MeshAdaptPUMI.h
MeshConverter.cpp
MeshFields.cpp
meshio.cpp
meshio.h
MeshSmoothing.cpp
MixedModelFactory.h
ModelFactory.h
mohrCoulomb.h
mohrCoulomb2.h
MoveMesh.cpp
MoveMesh.h
MoveMesh2D.cpp
MoveMesh2D.h
NCLS.cpp
NCLS.h
NCLS3P.cpp
NCLS3P.h
numericalFlux.c
numericalFlux.h	C implementations of numericalFlux calculations
NURBSshapes.f
ParallelMeshConverter.cpp
partitioning.cpp
partitioning.h
postprocessing.c
postprocessing.h	Python interface to velocity postprocessing library
Pres.cpp
Pres.h
PresInc.cpp
PresInc.h
PresInit.cpp
PresInit.h
ProtChBody.h
ProtChMoorings.h
proteus_blas.h
proteus_lapack.h
proteus_superlu.h
pskRelations.h
PyEmbeddedFunctions.h
RANS2P.cpp
RANS2P.h
RANS2P2D.cpp
RANS2P2D.h
RANS2P_IB.cpp
RANS2P_IB.h
RANS3PF.cpp
RANS3PF.h
RANS3PF2D.cpp
RANS3PF2D.h
RANS3PSed.cpp
RANS3PSed.h
RANS3PSed2D.cpp
RANS3PSed2D.h
RDLS.cpp
RDLS.h
Richards.h
SedClosure.cpp
SedClosure.h
shockCapturing.c
shockCapturing.h	C implementations of shock capturing diffusion calculations
SizeField.cpp
smoothers.c
smoothers.h	C implementations of multilevel smoother algorithms
Solve.cpp
sparsity.cpp
sparsity.h
subgridError.c
subgridError.h	C implementations of subgrid error calculations
Subroutines.cpp
SubsurfaceTransportCoefficients.cpp
SubsurfaceTransportCoefficients.h
subsurfaceTransportFunctions.c
superluWrappers.c
SW2D.cpp
SW2D.h
SW2DCV.cpp
SW2DCV.h
swigpyobject.h
testDomain.cpp
testFMMandFSW.cpp
testMesh.cpp
timeIntegration.c
timeIntegration.h	C interface for implementation of time discretization algorithms
transportCoefficients.c
transportCoefficients.h
tresca.h
twophaseDarcyCoefficients.h
Util.cpp
VMS.cpp
VOF.cpp
VOF.h
VOF3P.cpp
VOF3P.h
vonMises.h
VOS3P.cpp
VOS3P.h
WaveTools.cpp
WaveTools.h