What's actually here

A clone has four things in it:

Makefile      compile, link, convert to a flash image, flash it
main.c        your program
esp32s3/      the support library - the chip and this board
examples/     one runnable program per peripheral

examples/ is reference material, not a dependency. Delete the directory and make still builds main.c against the library exactly as before.

Everything that knows about the chip lives in esp32s3/, so a program stays readable as just the program. Write yours in main.c, include board.h (the umbrella) plus whatever peripheral drivers you need on top — led.h for the onboard RGB LED — and never touch a register directly.

File	Job
`main.c`	Your program. A skeleton: boot the chip, then stop
`examples/`	One runnable program per peripheral — see its own README
`esp32s3/include/`	The headers: the whole API surface
`esp32s3/src/board.c`	`board_init()` — zero .bss, disable watchdogs, raise the clock
`esp32s3/src/clock.c`	CPU clock: read it, switch to 160 MHz, ungate peripherals
`esp32s3/src/console.c`	Text over USB-Serial-JTAG
`esp32s3/src/delay.c`	Busy-wait timing
`esp32s3/src/gpio.c`	Digital pins, and the GPIO matrix peripherals reach them through
`esp32s3/src/uart.c`	Hardware serial ports
`esp32s3/src/i2c.c`	I2C master
`esp32s3/src/spi.c`	SPI master on GP-SPI2
`esp32s3/src/pwm.c`	PWM on the LEDC peripheral
`esp32s3/src/watchdog.c`	Disable the ROM's watchdogs
`esp32s3/src/led.c`	Addressable RGB LED (WS2812) bit-banging driver
`esp32s3/linker.ld`	Where the two segments land in SRAM
`Makefile`	Compile, link, convert to a flash image, flash it

main.c holds only board_init() and a halt. A program that does something is still just:

#include "board.h"
#include "led.h"

void _start(void)
{
    board_init();              /* .bss, watchdogs, 160 MHz */
    led_init(21);
    for (;;) {
        led_set_color(LED_RED);
        delay_ms(500);
        led_set_color(LED_OFF);
        delay_ms(500);
    }
}

Sizes, as text in the linked image:

Program	Size
`main.c` — boot and halt	352 B
the blink above	980 B
`examples/gpio_button.c`	1.4 KB
a program using all four buses	5.4 KB

Every driver is compiled every time, but --gc-sections drops each one the program never calls, so an unused bus costs nothing.