Here is a list of all topics with brief descriptions:

[detail level 12]

Power Management Controller (PMC)
Legacy PMC group alias
Legacy PMC group alias (alternate name)
Legacy ASF PMC group alias
System Clock Management (sysclock)
Legacy clock management group alias
Common stdio utilities
Standard serial I/O (stdio)	Common standard serial I/O management driver that implements a stdio serial interface on AVR and SAM devices
Peripheral Parallel Input/Output (PIO) Controller
Legacy PIO group alias
Busy-Wait Delay Routines	This module provides simple loop-based delay routines for those applications requiring a brief wait during execution
General Purpose Input/Output	This is the common API for GPIO
Legacy ASF GPIO group alias
Common IOPORT API	See Quick start guide for the common IOPORT service
SAM3/4S/4L/4E/4N/4CM/4C/G Timer Counter (TC) Driver	This driver for Atmel® \| SMART ARM®-based microcontrollers provides an interface for the configuration and management of the device's Timer Counter functionality
Global interrupt management	This is a driver for global enabling and disabling of interrupts
Deprecated interrupt definitions
Universal Synchronous Asynchronous Receiver	Transmitter (USART)
Universal Synchronous Asynchronous	Receiver Transmitter (USART)
Serial Interface (Serial)	See Quick start guide for Serial Interface service
Pulse Width Modulation (PWM)	See Quickstart guide for SAM PWM module
Two-Wire Interface (TWI)	Driver for the TWI (Two-Wire Interface)
Two Wire-interface(TWI)	This is the common API for TWIs
Serial Peripheral Interface (SPI)	See Quickstart guide for SAM SPI driver
Legacy SPI group alias
Analog-to-digital Converter (ADC)	See Quickstart guide for SAM ADC driver
Legacy ADC group alias
Timer Counter	SOFTWARE API DEFINITION FOR Timer Counter
SAM4SD32C definitions	This file defines all structures and symbols for SAM4SD32C:
CMSIS Definitions
Peripheral Software API	SOFTWARE PERIPHERAL API DEFINITION FOR SAM4SD32C
Registers Access Definitions
Peripheral Ids Definitions
Peripheral Base Address Definitions
Peripheral Pio Definitions
Parallel Input/Output Controller	SOFTWARE API DEFINITION FOR Parallel Input/Output Controller
Universal Synchronous Asynchronous Receiver Transmitter	SOFTWARE API DEFINITION FOR Universal Synchronous Asynchronous Receiver Transmitter
Pulse Width Modulation Controller	SOFTWARE API DEFINITION FOR Pulse Width Modulation Controller
Two-wire Interface	SOFTWARE API DEFINITION FOR Two-wire Interface
Serial Peripheral Interface	SOFTWARE API DEFINITION FOR Serial Peripheral Interface
Analog-to-Digital Converter	SOFTWARE API DEFINITION FOR Analog-to-Digital Converter