Here is a list of all files with brief descriptions:

[detail level 123]

docs
configuration
modules
include
atmega2560
ADC.h	ADC channels, multiplexer selections, references and modes
AnalogComparator.h	Analog comparator input and interrupt definitions
Architecture.h	AVR CPU architecture
ATmega2560.h	Aggregate include for all ATmega2560 definitions
Bootloader.h	Boot section sizes and Flash address ranges
Clock.h	Clock sources, oscillator and CPU prescaler
Config.h	Device, package and operating-grade selection
CPU.h	Core register and status flags
Device.h	Device identity and peripheral counts
EEPROM.h	EEPROM organization and endurance
Electrical.h	Operating conditions and absolute maximum ratings
Errata.h	Datasheet revision and device silicon errata references
ExternalInterrupts.h	External interrupt and pin-change mappings
Fuse.h	Low, high, and extended fuse bit locations
GPIO.h	GPIO port widths, masks and pull-ups
Interrupts.h	Interrupt vector sources, slot numbers and word addresses
JTAG.h	JTAG debug and boundary-scan interface
LockBits.h	Memory protection and bootloader lock bit positions
Memory.h	Flash, EEPROM, SRAM, and external-memory geometry
Package.h	Supported package types and selected package
PackagePins.h	Physical terminal and ball mappings for 100-terminal packages
Pin.h	Logical GPIO pin and port identifiers
PinFunctions.h	Pin capabilities and alternate function identifiers
Power.h	Sleep modes and peripheral power gates
Programming.h	In-system programming interface, signatures and page geometry
PWM.h	PWM output channels and associated logical pins
QTouch.h	Capacitive touch software support metadata
RegisterBits.h	Register bit positions and field masks
RegisterMap.h	Data-space addresses of ATmega2560 peripheral registers
Reset.h	Reset origins and status
RTC.h	Asynchronous Timer2 real-time counter support
SPI.h	SPI interface and pin definitions
Timer.h	Timer/counter architecture and modes
TWI.h	Two-wire serial interface characteristics
USART.h	USART frame modes, channel numbers and pin multiplexing
Watchdog.h	Watchdog oscillator and timeout selections
XMEM.h	External memory interface buses and control registers