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

platform
cores
phyduino
api
Common.h	Standard Arduino functions, constants and types (from ArduinoCore-API)
Arduino.h	Entry header for sketches: Arduino API + board pin map + Phyduino extras
RP2040.h	rp2040: the second core (setup1()/loop1()), the inter-core FIFO and chip information
SerialUART.h	Serial1, Serial2: the RP2040 hardware UARTs on the header pins
SerialUSB.h	Serial: USB CDC serial port (TinyUSB)
libraries
SPI
src
SPI.h	Arduino SPI on the header pins: SCK = D13, MOSI = D11, MISO = D12
Wire
src
Wire.h	Arduino Wire (I2C) on the SDA/SCL header pins
variants
phyduino_pico
max11635.h	Driver for the on-board MAX11635 12-bit ADC (U5)
pins_arduino.h	Phyduino Pico (RP2040): THE pin map. Every Arduino pin number and on-board peripheral pin is defined here and nowhere else
stusb4500.h	Driver for the on-board STUSB4500 USB Power Delivery sink controller (U6)