Here is a list of all files with brief descriptions:

[detail level 1234567]

common
services
delay
sam
cycle_counter.c	ARM functions for busy-wait delay loops
cycle_counter.h	ARM functions for busy-wait delay loops
delay.h	Common Delay Service
gpio
sam_gpio
sam_gpio.h	GPIO service for SAM
gpio.h	Common GPIO API
ioport
sam
ioport_pio.h	SAM architecture specific IOPORT service implementation header file
ioport.h	Common IOPORT service main header file for AVR, UC3 and ARM architectures
serial
sam_uart
uart_serial.h	Uart Serial for SAM
serial.h	Serial Mode management
usart_serial.c	USART Serial driver functions
twi
sam_twi
twi_master.h	TWI Master driver for SAM
twi_slave.h	TWI Slave driver for SAM
twi_master.h	TWI Master Mode management
twi_slave.h	TWI Slave Mode management
utils
interrupt
interrupt_sam_nvic.c	Global interrupt management for SAM D20, SAM3 and SAM4 (NVIC based)
interrupt_sam_nvic.h	Global interrupt management for SAM D20, SAM3 and SAM4 (NVIC based)
stdio
stdio_serial
stdio_serial.h	Common Standard I/O Serial Management
interrupt.h	Global interrupt management for 8- and 32-bit AVR
docs
sam
drivers
adc
adc.c	Analog-to-Digital Converter (ADC/ADC12B) driver for SAM
adc.h	Analog-to-Digital Converter (ADC/ADC12B) driver for SAM
pio
pio.c	Parallel Input/Output (PIO) Controller driver for SAM
pio.h	Parallel Input/Output (PIO) Controller driver for SAM
pio_handler.c	Parallel Input/Output (PIO) interrupt handler for SAM
pio_handler.h	Parallel Input/Output (PIO) interrupt handler for SAM
pwm
pwm.c	Pulse Width Modulation (PWM) driver for SAM
pwm.h	Pulse Width Modulation (PWM) driver for SAM
spi
spi.c	Serial Peripheral Interface (SPI) driver for SAM
spi.h	Serial Peripheral Interface (SPI) driver for SAM
tc
tc_capture_waveform_example
tc_capture_waveform_example.h	TC Capture Waveform Example for SAM
tc.c	SAM Timer Counter (TC) driver
tc.h	SAM Timer Counter (TC) driver
twi
twi.c	Two-Wire Interface (TWI) driver for SAM
twi.h	Two-Wire Interface (TWI) driver for SAM
usart
usart.c	Universal Synchronous Asynchronous Receiver Transmitter (USART) driver for SAM
usart.h	Universal Synchronous Asynchronous Receiver Transmitter (USART) driver for SAM
utils
cmsis
sam4s
include
component
component_adc.h	Copyright (c) 2012-2018 Microchip Technology Inc
component_pio.h	Copyright (c) 2012-2018 Microchip Technology Inc
component_pwm.h	Copyright (c) 2012-2018 Microchip Technology Inc
component_spi.h	Copyright (c) 2012-2018 Microchip Technology Inc
component_tc.h	Copyright (c) 2012-2018 Microchip Technology Inc
component_twi.h	Copyright (c) 2012-2018 Microchip Technology Inc
component_usart.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance
instance_adc.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_pioa.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_piob.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_pioc.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_pwm.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_spi.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_tc0.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_tc1.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_twi0.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_twi1.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_usart0.h	Copyright (c) 2012-2018 Microchip Technology Inc
instance_usart1.h	Copyright (c) 2012-2018 Microchip Technology Inc
pio
pio_sam4sd32c.h	Copyright (c) 2012-2018 Microchip Technology Inc
sam4sd32c.h	Copyright (c) 2012-2018 Microchip Technology Inc