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

src
PCSC
debuglog.h	This handles debugging
ifdhandler.h
pcsclite.h	This keeps a list of defines for pcsc-lite
reader.h	This keeps a list of defines shared between the driver and the application
winscard.h	This handles smart card reader communications
wintypes.h	This keeps a list of Windows(R) types
spy
libpcscspy.c
atrhandler.c	This keeps track of smart card protocols, timing issues and ATR (Answer-to-Reset) handling
atrhandler.h	This keeps track of smart card protocols, timing issues and Answer to Reset ATR handling
auth.c	Polkit authorization of clients
auth.h
configfile.c
configfile.h
debug.c	This handles debugging for libpcsclite
debuglog.c	This handles debugging for pcscd
dyn_generic.h	This abstracts dynamic library loading functions
dyn_hpux.c
dyn_macosx.c	This abstracts dynamic library loading functions and timing
dyn_unix.c	This abstracts dynamic library loading functions and timing
error.c	This handles pcsc_stringify_error()
eventhandler.c	This keeps track of card insertion/removal events and updates ATR, protocol, and status information
eventhandler.h	This handles card insertion/removal events, updates ATR, protocol, and status information
hotplug.h	This provides a search API for hot pluggble devices
hotplug_generic.c	This provides a search API for hot pluggble devices
hotplug_libudev.c	This provides a search API for hot pluggable devices using libudev
hotplug_libusb.c	This provides a search API for hot pluggble devices
hotplug_macosx.c	This provides a search API for hot pluggble devices
ifdwrapper.c	This wraps the dynamic ifdhandler functions
ifdwrapper.h	This wraps the dynamic ifdhandler functions
lassert.h
misc.h
parser.h	Reads lexical config files and updates database
pcsc-wirecheck-dist.c
pcsc-wirecheck-gen.c
pcsc-wirecheck-main.c
pcscd.h	This keeps a list of defines for pcsc-lite
pcscdaemon.c	This is the main pcscd daemon
prothandler.c	This handles protocol defaults, PTS, etc
prothandler.h	This handles protocol defaults, PTS, etc
readerfactory.c	This keeps track of a list of currently available reader structures
readerfactory.h	This keeps track of a list of currently available reader structures
simclist.c
simclist.h
sys_generic.h	This handles abstract system level calls
sys_unix.c	This handles abstract system level calls
testpcsc.c	This is a test program for pcsc-lite
tokenparser.c	Parsing functions for Info.plist files platforms
utils.c	Utility functions
utils.h
winscard.c	This handles smart card reader communications
winscard_clnt.c
winscard_msg.c	This is responsible for client/server communication
winscard_msg.h	This defines some structures and #defines to be used over the transport layer
winscard_msg_srv.c	Client/server communication (on the server side only)
winscard_svc.c	This demarshalls functions over the message queue and keeps track of clients and their handles
winscard_svc.h	This demarshalls functions over the message queue and keeps track of clients and their handles