Here is a list of all files with brief descriptions:

Documentation
jo_engine
jo
3d.h	Jo Engine 3D basics
audio.h	Jo Engine Function prototypes for audio
background.h	Jo Engine Background definition and tools
backup.h	Jo Engine saving features function prototypes
cell.h	Cells and portals: the rooms of an inside level (sections CELL and PRTL, see Documentation/level_format.md)
colors.h	Jo Engine Standard colors
conf.h	Jo Engine Internal configuration
console.h	Jo Engine Console function prototypes
console_builtins.h	Jo Engine Internal Console commands
core.h	Jo Engine core function prototypes
dsp.h	SCU DSP: the third processor of the Saturn (about 14 MHz, one 32 x 32 bits multiply and accumulate per cycle)
effects.h	Jo Engine Function prototypes special effects (Laser beam, fire, smoke, flash, shake, etc)
entity.h	Entities: the things of a level that live (barrels that explode, trigger zones, relays, doors, enemies...). They are read from a level (sections ENTI, PROP and LINK, see Documentation/level_format.md)
font.h	Jo Engine Simple ASCII Font & print support
fs.h	Jo Engine File System function prototypes
glow.h	Jo Engine glows: the halo of light around a lamp (a soft disc of its color, without edge, and a few thin rays of light, added to the image)
hitbox.h	Jo Engine Hitbox and tools
image.h	Jo Engine Image definition and tools
input.h	Jo Engine Gamepad functions
jo.h	Jo Engine Main Header
keyboard.h	Jo Engine Keyboard function prototypes
level.h	Levels (.JOL files): the data of a level of a game (terrain, models, plants, decals...), see Documentation/level_format.md. The files are written by the Python tools of Compiler/COMMON/jo_level
level_format.h
light.h	Jo Engine point lights: light sources (a position, a color, a radius, a strength; all around like a bulb or in a cone like a torch) that light the static meshes (in world coordinates: the rooms of the cells, the buildings...) through their gouraud tables (no sprite: the colors of the corners of the polygons)
list.h	Jo Engine Linked list helper
malloc.h	Jo Engine Malloc
map.h	Jo Engine MAP file (sprite map)
math.h	Jo Engine Math tools
mode7.h	Jo Engine Mode7
model.h	3D models (.JOM files): meshes made with a 3D software, converted by Compiler/COMMON/jo_model.py
palette.h	Jo Engine Palette Handling
physics.h	Jo Engine File Physics function prototypes
profile.h	Jo Engine profiler: time spent by the CPUs and the VDP1 in each frame
sega_saturn.h	Jo Engine Sega Saturn constants (addresses, memory sizes, etc)
serial.h
smpc.h	System Management & Peripheral Control
software_renderer.h	Fast Triangle based software renderer using fixed number
sprite_animator.h	Jo Engine Sprite Animator
sprites.h	Jo Engine Sprite definition and tools
storyboard.h	Jo Engine Storyboard Animation function prototypes
tga.h	Jo Engine Truevision Targa format support
time.h	Time Management
tools.h	Jo Engine Tools (printf, etc,)
types.h	Jo Engine Types
vcd_card.h	WIP VCD Card support
vdp1_command_pipeline.h	VDP1 command table handling
vdp2.h	Jo Engine VDP2 definition and tools
vdp2_malloc.h	VDP2 memory allocation (cell, map, rotation, scroll, etc)
vehicle.h	Vehicles: entities of the class vehicle (a jeep, a truck), driven by the player. An actor (a model with a rigid skeleton, see jo_3d_model_draw_pose()): the bones of the wheels turn, the bones of the front wheels and of the steering wheel steer. A simple physics: the speed (engine, brakes, drag), the steering (the turn radius comes from the wheelbase), the 4 wheels on the ground (the height, the pitch and the roll of the body follow the ground under them, with a little suspension), the collisions (the ground says where it can't go, the solid entities stop it: a hit at speed damages them)
video.h	Jo Engine Video Player (Sega FILM/CPK File Format)
voxel.h	Jo Engine Voxel renderer
weapon.h	Weapons of the player: the definitions (section WEAP of a level, for instance a file of definitions shared by the levels, see Documentation/level_format.md) and their rules: ammunition, fire rate (automatic or one shot per press), reload, change of weapon. The game draws the weapon of jo_weapons_current() and makes the shots (the bullets, the sounds, the flash) on the events of jo_weapons_update()