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

src
MatrixFree
ml_MatrixFreePreconditioner.h
MLAPI
MLAPI_Aggregation.h	Functions to create aggregation-based prolongator operators
MLAPI_BaseLinearCombination.h	Base class for all operator overloading related operations
MLAPI_BaseObject.h	Base MLAPI object
MLAPI_BaseOperator.h	Base MLAPI operator
MLAPI_CompObject.h	Class to count flops
MLAPI_Defaults.h	Function to set default values in a parameter list
MLAPI_DistributedMatrix.h	MLAPI wrapper for Epetra_FECrsMatrix, which allows MATLAB-like syntax
MLAPI_Eig.h	MLAPI interfaces to eigensolvers
MLAPI_EpetraBaseOperator.h	Basic class to wrap MLAPI::InverseOperator into Epetra_Operator
MLAPI_Expressions.h	Overloaded operators for MultiVector's, Operator's, and InverseOpereator's
MLAPI_Gallery.h	MLAPI interface to the Galeri package
MLAPI_InverseOperator.h	Base class for smoothers and coarse solvers
MLAPI_Krylov.h	MLAPI interface to AztecOO's solvers
MLAPI_LoadBalanceInverseOperator.h	Wraps an MLAPI inverseoperator with zero rows on some processors
MLAPI_LoadBalanceOperator.h	Wraps an MLAPI operator with zero rows on some processors
MLAPI_MATLABStream.h	Basic stream to save in a MATLAB-compatible file MLAPI objects
MLAPI_MultiLevelAdaptiveSA.h	Adaptive smoothed aggregation preconditioner
MLAPI_MultiLevelSA.h	Standard smoothed aggregation multilevel preconditioner
MLAPI_MultiVector.h	MLAPI wrapper for double vectors
MLAPI_MultiVector_Utils.h	Utilities for MultiVector's
MLAPI_Operator.h	Basic class to define operators within MLAPI
MLAPI_Operator_Box.h	Wrapper for ML_Operator to make it suitable for RefCountPtr
MLAPI_Operator_Utils.h	Suite of utilities for MLAPI::Operator objects
MLAPI_SerialMatrix.h	MATLAB-like serial matrix
MLAPI_Space.h	Class to specify the number and distribution among processes of elements
MLAPI_Workspace.h	Collection of utilities for workspace
RefMaxwell
ml_EdgeMatrixFreePreconditioner.h
ml_RefMaxwell.h
ml_RefMaxwell_11_Operator.h
Utils
ml_amesos_wrap.h	Interface to the Trilinos package Amesos
ml_anasazi.h	Interface to the Trilinos package Anasazi
ml_epetra_utils.h	Interface to the Trilinos package Anasazi
ml_Epetra_wrap_CrsGraph_as_RowMatrix.H
ml_Ifpack_ML.h
ml_ifpack_wrap.h	Interface to the Trilinos package Ifpack
ml_MultiLevelOperator.h	Defines an ML preconditioner as a Epetra_Operator derived class
ml_MultiLevelPreconditioner.cpp	ML black-box preconditioner for Epetra_RowMatrix derived classes
ml_MultiLevelPreconditioner.h
ml_MultiLevelPreconditioner_Adapt.cpp	Methods to define adaptive smoothed aggregation
ml_MultiLevelPreconditioner_Analyze.cpp	Visualization utilities for MultiLevelPreconditioner class
ml_MultiLevelPreconditioner_Defaults.cpp	ML black-box defaults for Epetra_RowMatrix derived classes
ml_MultiLevelPreconditioner_Smoothers.cpp	ML black-box preconditioner for Epetra_RowMatrix derived classes
ml_MultiLevelPreconditioner_Viz.cpp	Visualization utilities for MultiLevelPreconditioner class
ml_MultiLevelPreconditioner_XML.cpp	Converter from an XML file to internally stored Teuchos::ParameterList
ml_RowMatrix.h	Wrapper from ML_Operator to Epetra_RowMatrix