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

include
FLAC
all.h
assert.h
callback.h	This module defines the structures for describing I/O callbacks to the other FLAC interfaces
export.h	This module contains #defines and symbols for exporting function calls, and providing version information and compiled-in features
format.h	This module contains structure definitions for the representation of FLAC format components in memory. These are the basic structures used by the rest of the interfaces
metadata.h	This module provides functions for creating and manipulating FLAC metadata blocks in memory, and three progressively more powerful interfaces for traversing and editing metadata in FLAC files
ordinals.h
stream_decoder.h	This module contains the functions which implement the stream decoder
stream_encoder.h	This module contains the functions which implement the stream encoder
FLAC++
all.h
decoder.h	This module contains the classes which implement the various decoders
encoder.h	This module contains the classes which implement the various encoders
export.h	This module contains #defines and symbols for exporting function calls, and providing version information and compiled-in features
metadata.h	This module provides classes for creating and manipulating FLAC metadata blocks in memory, and three progressively more powerful interfaces for traversing and editing metadata in FLAC files